Starting phenix.real_space_refine on Wed Sep 17 19:10:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xk4_38415/09_2025/8xk4_38415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xk4_38415/09_2025/8xk4_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_38415/09_2025/8xk4_38415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xk4_38415/09_2025/8xk4_38415.map" model { file = "/net/cci-nas-00/data/ceres_data/8xk4_38415/09_2025/8xk4_38415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xk4_38415/09_2025/8xk4_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-2.0-5805/lib/python3.9/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: 1.76, per 1000 atoms: 0.29 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: 0.63 Conformation dependent library (CDL) restraints added in 313.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.71 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: 1.25 Time building geometry restraints manager: 0.82 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=" N SER A 611 " pdb=" CA SER A 611 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.82e+00 bond pdb=" CA SER A 611 " pdb=" CB SER A 611 " ideal model delta sigma weight residual 1.528 1.490 0.039 1.59e-02 3.96e+03 5.89e+00 ... (remaining 6215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 8267 1.61 - 3.22: 188 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=" 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=" N SER A 611 " pdb=" CA SER A 611 " pdb=" C SER A 611 " ideal model delta sigma weight residual 111.36 107.17 4.19 1.09e+00 8.42e-01 1.48e+01 angle pdb=" N ILE A 268 " pdb=" CA ILE A 268 " pdb=" C ILE A 268 " ideal model delta sigma weight residual 113.20 109.53 3.67 9.60e-01 1.09e+00 1.46e+01 angle pdb=" N VAL A 264 " pdb=" CA VAL A 264 " pdb=" C VAL A 264 " ideal model delta sigma weight residual 113.07 107.90 5.17 1.36e+00 5.41e-01 1.44e+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 - 0.107: 919 0.107 - 0.213: 25 0.213 - 0.320: 1 0.320 - 0.426: 0 0.426 - 0.533: 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 2.35 2.88 -0.53 2.00e-01 2.50e+01 7.10e+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 2.35 -2.84 -0.50 2.00e-01 2.50e+01 6.18e+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 2.35 2.61 -0.27 2.00e-01 2.50e+01 1.78e+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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.700 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 6220 Z= 0.206 Angle : 0.634 8.046 8499 Z= 0.370 Chirality : 0.050 0.533 947 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 aren 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 covalent geometry : bond 0.00432 ( 6220) covalent geometry : angle 0.63390 ( 8499) hydrogen bonds : bond 0.19063 ( 239) hydrogen bonds : angle 7.20322 ( 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 : 0.226 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: 0.5464 time to fit residues: 76.1381 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 : 0.195 ------------------------------------------------------------------------------- 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: 0.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4086 r_free = 0.4086 target = 0.187135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.149204 restraints weight = 6210.876| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.80 r_work: 0.3432 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6220 Z= 0.147 Angle : 0.562 6.612 8499 Z= 0.311 Chirality : 0.044 0.176 947 Planarity : 0.005 0.054 1002 Dihedral : 12.995 140.380 978 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.32 % Allowed : 12.91 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.32), residues: 681 helix: -0.13 (0.37), residues: 221 sheet: 0.98 (0.46), residues: 143 loop : -1.46 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 105 TYR 0.019 0.001 TYR A 37 PHE 0.024 0.002 PHE A 351 TRP 0.008 0.001 TRP A 282 HIS 0.005 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6220) covalent geometry : angle 0.56230 ( 8499) hydrogen bonds : bond 0.04273 ( 239) hydrogen bonds : angle 4.82978 ( 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 112 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.155 Fit side-chains REVERT: A 56 HIS cc_start: 0.7789 (m-70) cc_final: 0.7310 (m170) REVERT: A 310 ASP cc_start: 0.6794 (m-30) cc_final: 0.6486 (m-30) REVERT: A 371 LYS cc_start: 0.8147 (tppt) cc_final: 0.7866 (mmmt) REVERT: A 432 ARG cc_start: 0.6334 (mtm-85) cc_final: 0.6059 (mtp85) REVERT: A 539 MET cc_start: 0.8029 (mpp) cc_final: 0.7735 (mmt) REVERT: A 731 GLN cc_start: 0.7277 (mm-40) cc_final: 0.7003 (tp-100) outliers start: 14 outliers final: 2 residues processed: 105 average time/residue: 0.4895 time to fit residues: 54.2149 Evaluate side-chains 85 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 424 THR 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: 4.9990 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 35 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3985 r_free = 0.3985 target = 0.178065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.139764 restraints weight = 6191.351| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.70 r_work: 0.3367 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6220 Z= 0.187 Angle : 0.588 6.491 8499 Z= 0.322 Chirality : 0.045 0.178 947 Planarity : 0.004 0.046 1002 Dihedral : 13.189 138.256 976 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.64 % Allowed : 14.74 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.32), residues: 681 helix: -0.18 (0.36), residues: 219 sheet: 1.02 (0.46), residues: 137 loop : -1.60 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 275 TYR 0.019 0.001 TYR A 37 PHE 0.021 0.002 PHE A 351 TRP 0.006 0.001 TRP A 282 HIS 0.006 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 6220) covalent geometry : angle 0.58760 ( 8499) hydrogen bonds : bond 0.04802 ( 239) hydrogen bonds : angle 4.85448 ( 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 109 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.177 Fit side-chains REVERT: A 274 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7946 (mmtp) REVERT: A 310 ASP cc_start: 0.7001 (m-30) cc_final: 0.6674 (m-30) REVERT: A 371 LYS cc_start: 0.8161 (tppt) cc_final: 0.7865 (mmmt) REVERT: A 540 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7706 (tpp) REVERT: A 643 ARG cc_start: 0.7622 (ttm-80) cc_final: 0.7167 (mtt180) REVERT: A 719 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.7691 (t80) outliers start: 22 outliers final: 10 residues processed: 98 average time/residue: 0.4243 time to fit residues: 43.9519 Evaluate side-chains 90 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU 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 436 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.0370 chunk 45 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4042 r_free = 0.4042 target = 0.183103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.147539 restraints weight = 6258.369| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.75 r_work: 0.3481 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2821 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= 0.126 Angle : 0.511 5.700 8499 Z= 0.282 Chirality : 0.042 0.184 947 Planarity : 0.004 0.041 1002 Dihedral : 12.961 137.173 976 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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 aren not related in a simple way. whole: -0.65 (0.32), residues: 681 helix: 0.01 (0.36), residues: 224 sheet: 1.13 (0.45), residues: 137 loop : -1.47 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 291 TYR 0.014 0.001 TYR A 37 PHE 0.016 0.001 PHE A 319 TRP 0.005 0.001 TRP A 512 HIS 0.005 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6220) covalent geometry : angle 0.51109 ( 8499) hydrogen bonds : bond 0.03711 ( 239) hydrogen bonds : angle 4.55856 ( 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 105 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.168 Fit side-chains REVERT: A 310 ASP cc_start: 0.6914 (m-30) cc_final: 0.6573 (m-30) REVERT: A 371 LYS cc_start: 0.8190 (tppt) cc_final: 0.7928 (mmmt) REVERT: A 432 ARG cc_start: 0.6545 (mtm-85) cc_final: 0.6282 (mtp85) REVERT: A 643 ARG cc_start: 0.7633 (ttm-80) cc_final: 0.7146 (mtt180) REVERT: A 678 LYS cc_start: 0.8131 (pmmt) cc_final: 0.7430 (tppt) REVERT: A 719 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7583 (t80) outliers start: 19 outliers final: 7 residues processed: 97 average time/residue: 0.4442 time to fit residues: 45.6799 Evaluate side-chains 84 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 320 HIS Chi-restraints excluded: chain A residue 424 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 60 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4006 r_free = 0.4006 target = 0.179605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.140429 restraints weight = 6375.864| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.94 r_work: 0.3331 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3071 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= 0.193 Angle : 0.586 6.231 8499 Z= 0.320 Chirality : 0.045 0.194 947 Planarity : 0.004 0.047 1002 Dihedral : 13.215 138.914 976 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.31 % Allowed : 17.72 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.32), residues: 681 helix: -0.15 (0.35), residues: 222 sheet: 1.03 (0.45), residues: 137 loop : -1.59 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 275 TYR 0.014 0.001 TYR A 37 PHE 0.022 0.002 PHE A 319 TRP 0.005 0.001 TRP A 282 HIS 0.005 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 6220) covalent geometry : angle 0.58644 ( 8499) hydrogen bonds : bond 0.04597 ( 239) hydrogen bonds : angle 4.86451 ( 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 99 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.162 Fit side-chains REVERT: A 274 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7604 (mppt) REVERT: A 310 ASP cc_start: 0.7050 (m-30) cc_final: 0.6704 (m-30) REVERT: A 371 LYS cc_start: 0.8086 (tppt) cc_final: 0.7814 (mmmt) REVERT: A 432 ARG cc_start: 0.6543 (mtm-85) cc_final: 0.6278 (mtp85) REVERT: A 540 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7831 (tpp) REVERT: A 608 LYS cc_start: 0.7957 (tppp) cc_final: 0.7656 (ttpt) REVERT: A 643 ARG cc_start: 0.7708 (ttm-80) cc_final: 0.7256 (mtt180) REVERT: A 678 LYS cc_start: 0.8094 (pmmt) cc_final: 0.7411 (tppt) REVERT: A 719 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7633 (t80) outliers start: 20 outliers final: 8 residues processed: 92 average time/residue: 0.4476 time to fit residues: 43.8177 Evaluate side-chains 87 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 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 540 MET 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: 0.9990 chunk 3 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4006 r_free = 0.4006 target = 0.179997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.141592 restraints weight = 6214.886| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.83 r_work: 0.3428 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6220 Z= 0.148 Angle : 0.546 6.497 8499 Z= 0.296 Chirality : 0.044 0.224 947 Planarity : 0.004 0.046 1002 Dihedral : 13.089 138.263 976 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.31 % Allowed : 19.21 % 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 aren not related in a simple way. whole: -0.81 (0.32), residues: 681 helix: -0.16 (0.35), residues: 227 sheet: 1.01 (0.45), residues: 137 loop : -1.53 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 291 TYR 0.013 0.001 TYR A 37 PHE 0.018 0.002 PHE A 319 TRP 0.005 0.001 TRP A 512 HIS 0.005 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6220) covalent geometry : angle 0.54586 ( 8499) hydrogen bonds : bond 0.04021 ( 239) hydrogen bonds : angle 4.66455 ( 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 102 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.231 Fit side-chains REVERT: A 133 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8368 (tt) REVERT: A 310 ASP cc_start: 0.6919 (m-30) cc_final: 0.6563 (m-30) REVERT: A 371 LYS cc_start: 0.8083 (tppt) cc_final: 0.7851 (mmmt) REVERT: A 432 ARG cc_start: 0.6611 (mtm-85) cc_final: 0.6389 (mtp85) REVERT: A 608 LYS cc_start: 0.7854 (tppp) cc_final: 0.7559 (ttpt) REVERT: A 643 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7304 (mtt180) REVERT: A 678 LYS cc_start: 0.8187 (pmmt) cc_final: 0.7514 (tppt) REVERT: A 719 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7647 (t80) outliers start: 20 outliers final: 8 residues processed: 93 average time/residue: 0.4461 time to fit residues: 44.1417 Evaluate side-chains 85 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 151 THR 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 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: 3.9990 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 chunk 1 optimal weight: 0.0980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4020 r_free = 0.4020 target = 0.180837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.142596 restraints weight = 6232.171| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.88 r_work: 0.3388 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3394 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= 0.202 Angle : 0.608 7.793 8499 Z= 0.327 Chirality : 0.046 0.207 947 Planarity : 0.004 0.050 1002 Dihedral : 13.312 139.987 976 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.31 % Allowed : 19.87 % 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 aren not related in a simple way. whole: -0.95 (0.31), residues: 681 helix: -0.26 (0.35), residues: 224 sheet: 0.93 (0.45), residues: 137 loop : -1.62 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 275 TYR 0.014 0.001 TYR A 37 PHE 0.026 0.002 PHE A 319 TRP 0.006 0.001 TRP A 512 HIS 0.005 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 6220) covalent geometry : angle 0.60795 ( 8499) hydrogen bonds : bond 0.04766 ( 239) hydrogen bonds : angle 4.83219 ( 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 99 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.233 Fit side-chains REVERT: A 274 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7684 (mppt) REVERT: A 310 ASP cc_start: 0.7035 (m-30) cc_final: 0.6695 (m-30) REVERT: A 371 LYS cc_start: 0.8059 (tppt) cc_final: 0.7800 (mmmt) REVERT: A 432 ARG cc_start: 0.6608 (mtm-85) cc_final: 0.6317 (mtp85) REVERT: A 608 LYS cc_start: 0.7890 (tppp) cc_final: 0.7580 (ttpt) REVERT: A 643 ARG cc_start: 0.7751 (ttm-80) cc_final: 0.7346 (mtt180) REVERT: A 678 LYS cc_start: 0.8101 (pmmt) cc_final: 0.7459 (tppt) REVERT: A 719 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7706 (t80) outliers start: 20 outliers final: 8 residues processed: 94 average time/residue: 0.4633 time to fit residues: 46.1867 Evaluate side-chains 83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 53 TYR 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 424 THR 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: 0.9990 chunk 21 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 149 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 = 0.180589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143898 restraints weight = 6261.484| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.77 r_work: 0.3385 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3462 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= 0.133 Angle : 0.536 7.120 8499 Z= 0.291 Chirality : 0.043 0.188 947 Planarity : 0.004 0.048 1002 Dihedral : 13.043 138.469 976 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.65 % Allowed : 21.52 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.32), residues: 681 helix: -0.06 (0.35), residues: 227 sheet: 1.00 (0.45), residues: 137 loop : -1.48 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 291 TYR 0.013 0.001 TYR A 37 PHE 0.016 0.001 PHE A 319 TRP 0.010 0.001 TRP A 512 HIS 0.005 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6220) covalent geometry : angle 0.53616 ( 8499) hydrogen bonds : bond 0.03790 ( 239) hydrogen bonds : angle 4.57670 ( 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 96 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.262 Fit side-chains REVERT: A 13 ARG cc_start: 0.7341 (mtm110) cc_final: 0.6959 (mpt90) REVERT: A 274 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7551 (mppt) REVERT: A 289 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7797 (mm-40) REVERT: A 310 ASP cc_start: 0.6972 (m-30) cc_final: 0.6592 (m-30) REVERT: A 371 LYS cc_start: 0.7979 (tppt) cc_final: 0.7705 (mmmt) REVERT: A 432 ARG cc_start: 0.6522 (mtm-85) cc_final: 0.6277 (mtp85) REVERT: A 608 LYS cc_start: 0.7809 (tppp) cc_final: 0.7494 (ttpt) REVERT: A 643 ARG cc_start: 0.7721 (ttm-80) cc_final: 0.7293 (mtt180) REVERT: A 678 LYS cc_start: 0.8101 (pmmt) cc_final: 0.7442 (tppt) REVERT: A 700 MET cc_start: 0.7801 (mtp) cc_final: 0.7492 (mtp) REVERT: A 719 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.7537 (t80) outliers start: 16 outliers final: 7 residues processed: 90 average time/residue: 0.4183 time to fit residues: 40.0044 Evaluate side-chains 87 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR 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 289 GLN Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR 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: 2.9990 chunk 41 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 20 optimal weight: 0.0570 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4004 r_free = 0.4004 target = 0.180121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.142608 restraints weight = 6294.123| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.86 r_work: 0.3364 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6220 Z= 0.139 Angle : 0.549 8.954 8499 Z= 0.299 Chirality : 0.043 0.197 947 Planarity : 0.004 0.046 1002 Dihedral : 13.009 138.494 976 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.15 % Allowed : 22.19 % Favored : 75.66 % 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 aren not related in a simple way. whole: -0.64 (0.32), residues: 681 helix: 0.08 (0.35), residues: 223 sheet: 1.03 (0.45), residues: 137 loop : -1.45 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 291 TYR 0.014 0.001 TYR A 37 PHE 0.017 0.001 PHE A 319 TRP 0.009 0.001 TRP A 512 HIS 0.005 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 6220) covalent geometry : angle 0.54927 ( 8499) hydrogen bonds : bond 0.03905 ( 239) hydrogen bonds : angle 4.66700 ( 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 94 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.216 Fit side-chains REVERT: A 133 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8335 (tt) REVERT: A 274 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7593 (mppt) REVERT: A 289 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7776 (mm-40) REVERT: A 310 ASP cc_start: 0.7019 (m-30) cc_final: 0.6634 (m-30) REVERT: A 371 LYS cc_start: 0.7988 (tppt) cc_final: 0.7721 (mmmt) REVERT: A 432 ARG cc_start: 0.6528 (mtm-85) cc_final: 0.6277 (mtp85) REVERT: A 608 LYS cc_start: 0.7802 (tppp) cc_final: 0.7502 (ttpt) REVERT: A 643 ARG cc_start: 0.7748 (ttm-80) cc_final: 0.7321 (mtt180) REVERT: A 678 LYS cc_start: 0.8043 (pmmt) cc_final: 0.7355 (tppt) REVERT: A 700 MET cc_start: 0.7895 (mtp) cc_final: 0.7565 (mtp) REVERT: A 719 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7554 (t80) outliers start: 13 outliers final: 7 residues processed: 90 average time/residue: 0.4175 time to fit residues: 40.0298 Evaluate side-chains 89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR 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: 2.9990 chunk 11 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 ASN A 548 HIS A 575 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.183428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.145330 restraints weight = 6225.072| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.74 r_work: 0.3459 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6220 Z= 0.124 Angle : 0.532 8.694 8499 Z= 0.289 Chirality : 0.043 0.184 947 Planarity : 0.004 0.045 1002 Dihedral : 12.875 137.427 976 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.99 % Allowed : 22.52 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.32), residues: 681 helix: 0.11 (0.35), residues: 226 sheet: 1.10 (0.45), residues: 143 loop : -1.39 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 291 TYR 0.013 0.001 TYR A 37 PHE 0.029 0.001 PHE A 86 TRP 0.012 0.001 TRP A 512 HIS 0.005 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6220) covalent geometry : angle 0.53230 ( 8499) hydrogen bonds : bond 0.03594 ( 239) hydrogen bonds : angle 4.57171 ( 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 100 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.222 Fit side-chains REVERT: A 67 MET cc_start: 0.7944 (tpt) cc_final: 0.7743 (mmt) REVERT: A 274 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7562 (mppt) REVERT: A 289 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7774 (mm-40) REVERT: A 310 ASP cc_start: 0.6885 (m-30) cc_final: 0.6496 (m-30) REVERT: A 371 LYS cc_start: 0.7967 (tppt) cc_final: 0.7723 (mmmt) REVERT: A 432 ARG cc_start: 0.6521 (mtm-85) cc_final: 0.6312 (mtp85) REVERT: A 608 LYS cc_start: 0.7834 (tppp) cc_final: 0.7559 (ttpt) REVERT: A 643 ARG cc_start: 0.7710 (ttm-80) cc_final: 0.7338 (mtt180) REVERT: A 678 LYS cc_start: 0.8068 (pmmt) cc_final: 0.7434 (tppt) REVERT: A 700 MET cc_start: 0.7862 (mtp) cc_final: 0.7485 (mtp) REVERT: A 719 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7489 (t80) outliers start: 12 outliers final: 6 residues processed: 95 average time/residue: 0.4317 time to fit residues: 43.5185 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 : 0.217 ------------------------------------------------------------------------------- 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 289 GLN Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR 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: 3.9990 chunk 5 optimal weight: 0.0980 chunk 42 optimal weight: 0.0970 chunk 7 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4027 r_free = 0.4027 target = 0.181763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.144196 restraints weight = 6136.290| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.89 r_work: 0.3414 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6220 Z= 0.168 Angle : 0.584 8.706 8499 Z= 0.316 Chirality : 0.044 0.222 947 Planarity : 0.004 0.049 1002 Dihedral : 13.034 138.780 976 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.66 % Allowed : 23.84 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.32), residues: 681 helix: 0.02 (0.35), residues: 223 sheet: 1.08 (0.45), residues: 143 loop : -1.43 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 275 TYR 0.013 0.001 TYR A 37 PHE 0.026 0.002 PHE A 86 TRP 0.009 0.001 TRP A 512 HIS 0.005 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6220) covalent geometry : angle 0.58364 ( 8499) hydrogen bonds : bond 0.04252 ( 239) hydrogen bonds : angle 4.72558 ( 647) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2355.20 seconds wall clock time: 40 minutes 46.99 seconds (2446.99 seconds total)