Starting phenix.real_space_refine on Thu Jul 2 07:09:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7b4l_12002/07_2026/7b4l_12002.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b4l_12002/07_2026/7b4l_12002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b4l_12002/07_2026/7b4l_12002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b4l_12002/07_2026/7b4l_12002.map" model { file = "/net/cci-nas-00/data/ceres_data/7b4l_12002/07_2026/7b4l_12002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b4l_12002/07_2026/7b4l_12002.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7b4l_12002/07_2026/7b4l_12002.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7b4l_12002/07_2026/7b4l_12002.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 36 5.16 5 Na 2 4.78 5 C 4740 2.51 5 N 1068 2.21 5 O 1180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s 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: 7030 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3300 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 423} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3300 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 423} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 202 Unusual residues: {' NA': 1, 'C14': 3, 'POV': 2, 'UND': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 202 Unusual residues: {' NA': 1, 'C14': 3, 'POV': 2, 'UND': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="NA NA A 601 " occ=0.50 residue: pdb="NA NA B 602 " occ=0.50 residue: pdb=" O HOH A 711 " occ=0.50 residue: pdb=" O HOH B 711 " occ=0.50 Time building chain proxies: 1.39, per 1000 atoms: 0.20 Number of scatterers: 7030 At special positions: 0 Unit cell: (97.643, 91.205, 77.256, 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) S 36 16.00 P 4 15.00 Na 2 11.00 O 1180 8.00 N 1068 7.00 C 4740 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: 0.61 Conformation dependent library (CDL) restraints added in 352.2 milliseconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 84.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 82 through 106 removed outlier: 3.510A pdb=" N ILE A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 110 Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 144 through 159 removed outlier: 3.982A pdb=" N GLY A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 169 through 190 Processing helix chain 'A' and resid 193 through 200 removed outlier: 3.517A pdb=" N LYS A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 224 Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 230 through 241 removed outlier: 3.523A pdb=" N ILE A 236 " --> pdb=" O GLN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 260 removed outlier: 3.644A pdb=" N VAL A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Proline residue: A 251 - end of helix removed outlier: 3.764A pdb=" N LEU A 255 " --> pdb=" O PRO A 251 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 274 removed outlier: 3.610A pdb=" N ALA A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 295 removed outlier: 3.737A pdb=" N ILE A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 327 removed outlier: 3.623A pdb=" N ASN A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 307 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 358 Processing helix chain 'A' and resid 361 through 378 removed outlier: 3.558A pdb=" N LEU A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 406 removed outlier: 3.641A pdb=" N ILE A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) Proline residue: A 398 - end of helix Processing helix chain 'A' and resid 418 through 440 removed outlier: 3.570A pdb=" N VAL A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 461 through 468 Processing helix chain 'A' and resid 469 through 479 Processing helix chain 'A' and resid 481 through 517 removed outlier: 4.086A pdb=" N ASP A 485 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Proline residue: A 503 - end of helix Proline residue: A 514 - end of helix Processing helix chain 'B' and resid 82 through 106 removed outlier: 3.510A pdb=" N ILE B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 110 Processing helix chain 'B' and resid 113 through 134 Processing helix chain 'B' and resid 144 through 159 removed outlier: 3.982A pdb=" N GLY B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 169 through 190 Processing helix chain 'B' and resid 193 through 200 removed outlier: 3.517A pdb=" N LYS B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 224 Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 230 through 241 removed outlier: 3.523A pdb=" N ILE B 236 " --> pdb=" O GLN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 260 removed outlier: 3.644A pdb=" N VAL B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Proline residue: B 251 - end of helix removed outlier: 3.764A pdb=" N LEU B 255 " --> pdb=" O PRO B 251 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 274 removed outlier: 3.611A pdb=" N ALA B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 295 removed outlier: 3.737A pdb=" N ILE B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 327 removed outlier: 3.623A pdb=" N ASN B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 307 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 327 " --> pdb=" O PHE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 358 Processing helix chain 'B' and resid 361 through 378 removed outlier: 3.558A pdb=" N LEU B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 406 removed outlier: 3.641A pdb=" N ILE B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) Proline residue: B 398 - end of helix Processing helix chain 'B' and resid 418 through 440 removed outlier: 3.570A pdb=" N VAL B 425 " --> pdb=" O CYS B 421 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 440 " --> pdb=" O THR B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 456 Processing helix chain 'B' and resid 461 through 468 Processing helix chain 'B' and resid 469 through 479 Processing helix chain 'B' and resid 481 through 517 removed outlier: 4.086A pdb=" N ASP B 485 " --> pdb=" O LYS B 481 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) Proline residue: B 503 - end of helix Proline residue: B 514 - end of helix 498 hydrogen bonds defined for protein. 1488 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.76 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1016 1.31 - 1.43: 1700 1.43 - 1.56: 4346 1.56 - 1.69: 8 1.69 - 1.81: 52 Bond restraints: 7122 Sorted by residual: bond pdb=" C31 POV A 602 " pdb=" O31 POV A 602 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C31 POV B 603 " pdb=" O31 POV B 603 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C31 POV B 601 " pdb=" O31 POV B 601 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C31 POV A 611 " pdb=" O31 POV A 611 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C21 POV B 603 " pdb=" O21 POV B 603 " ideal model delta sigma weight residual 1.330 1.400 -0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 7117 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 9129 2.43 - 4.87: 386 4.87 - 7.30: 31 7.30 - 9.74: 18 9.74 - 12.17: 8 Bond angle restraints: 9572 Sorted by residual: angle pdb=" O11 POV B 601 " pdb=" P POV B 601 " pdb=" O12 POV B 601 " ideal model delta sigma weight residual 97.67 109.84 -12.17 3.00e+00 1.11e-01 1.65e+01 angle pdb=" O11 POV A 611 " pdb=" P POV A 611 " pdb=" O12 POV A 611 " ideal model delta sigma weight residual 97.67 109.82 -12.15 3.00e+00 1.11e-01 1.64e+01 angle pdb=" O13 POV B 601 " pdb=" P POV B 601 " pdb=" O14 POV B 601 " ideal model delta sigma weight residual 121.11 109.21 11.90 3.00e+00 1.11e-01 1.57e+01 angle pdb=" O13 POV A 611 " pdb=" P POV A 611 " pdb=" O14 POV A 611 " ideal model delta sigma weight residual 121.11 109.21 11.90 3.00e+00 1.11e-01 1.57e+01 angle pdb=" O13 POV A 602 " pdb=" P POV A 602 " pdb=" O14 POV A 602 " ideal model delta sigma weight residual 121.11 109.62 11.49 3.00e+00 1.11e-01 1.47e+01 ... (remaining 9567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.04: 3822 20.04 - 40.08: 312 40.08 - 60.13: 78 60.13 - 80.17: 10 80.17 - 100.21: 2 Dihedral angle restraints: 4224 sinusoidal: 1754 harmonic: 2470 Sorted by residual: dihedral pdb=" CA TYR B 326 " pdb=" C TYR B 326 " pdb=" N PHE B 327 " pdb=" CA PHE B 327 " ideal model delta harmonic sigma weight residual -180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TYR A 326 " pdb=" C TYR A 326 " pdb=" N PHE A 327 " pdb=" CA PHE A 327 " ideal model delta harmonic sigma weight residual -180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA PHE A 327 " pdb=" C PHE A 327 " pdb=" N PRO A 328 " pdb=" CA PRO A 328 " ideal model delta harmonic sigma weight residual 180.00 161.65 18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 4221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 787 0.037 - 0.075: 307 0.075 - 0.112: 38 0.112 - 0.149: 10 0.149 - 0.187: 4 Chirality restraints: 1146 Sorted by residual: chirality pdb=" CB THR B 417 " pdb=" CA THR B 417 " pdb=" OG1 THR B 417 " pdb=" CG2 THR B 417 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CB THR A 417 " pdb=" CA THR A 417 " pdb=" OG1 THR A 417 " pdb=" CG2 THR A 417 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CG LEU B 483 " pdb=" CB LEU B 483 " pdb=" CD1 LEU B 483 " pdb=" CD2 LEU B 483 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.36e-01 ... (remaining 1143 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 110 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.45e+00 pdb=" N PRO A 111 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 111 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 111 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 110 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO B 111 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 111 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 111 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 502 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A 503 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 503 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 503 " -0.022 5.00e-02 4.00e+02 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 116 2.69 - 3.24: 6962 3.24 - 3.80: 10296 3.80 - 4.35: 14397 4.35 - 4.90: 24237 Nonbonded interactions: 56008 Sorted by model distance: nonbonded pdb=" O SER B 497 " pdb=" OG1 THR B 501 " model vdw 2.141 3.040 nonbonded pdb=" O SER A 497 " pdb=" OG1 THR A 501 " model vdw 2.141 3.040 nonbonded pdb=" O PHE B 445 " pdb=" NZ LYS B 450 " model vdw 2.282 3.120 nonbonded pdb=" O PHE A 445 " pdb=" NZ LYS A 450 " model vdw 2.283 3.120 nonbonded pdb=" O LYS B 450 " pdb=" OG SER B 454 " model vdw 2.297 3.040 ... (remaining 56003 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 79 through 521 or resid 604 through 605 or resid 607 throu \ gh 610)) selection = (chain 'B' and (resid 79 through 521 or resid 604 through 605 or resid 607 throu \ gh 610)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.800 Find NCS groups from input model: 0.090 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 0.072 7122 Z= 0.231 Angle : 1.048 12.169 9572 Z= 0.442 Chirality : 0.039 0.187 1146 Planarity : 0.005 0.053 1122 Dihedral : 15.907 100.208 2648 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.27), residues: 882 helix: -0.07 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.28 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 157 TYR 0.007 0.001 TYR B 123 PHE 0.009 0.001 PHE B 401 TRP 0.012 0.002 TRP A 378 HIS 0.001 0.000 HIS A 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.23 ( 7122) covalent geometry : angle 1.04846 / 0.44 ( 9572) hydrogen bonds : bond 0.26939 / 18.38 ( 498) hydrogen bonds : angle 8.22316 / 5.77 ( 1488) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.207 Fit side-chains REVERT: A 149 MET cc_start: 0.8974 (mtt) cc_final: 0.8530 (mtm) REVERT: A 198 LYS cc_start: 0.8365 (ttpt) cc_final: 0.7814 (mmtt) REVERT: A 489 ASP cc_start: 0.7389 (m-30) cc_final: 0.7154 (m-30) REVERT: B 149 MET cc_start: 0.8975 (mtt) cc_final: 0.8530 (mtm) REVERT: B 198 LYS cc_start: 0.8367 (ttpt) cc_final: 0.7821 (mmtt) REVERT: B 489 ASP cc_start: 0.7391 (m-30) cc_final: 0.7153 (m-30) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0670 time to fit residues: 11.0347 Evaluate side-chains 88 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.143974 restraints weight = 8886.368| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.75 r_work: 0.3726 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.3627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7122 Z= 0.138 Angle : 0.639 9.258 9572 Z= 0.320 Chirality : 0.041 0.145 1146 Planarity : 0.005 0.055 1122 Dihedral : 14.112 98.875 1212 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.40 % Allowed : 7.28 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.29), residues: 882 helix: 1.03 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -2.14 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 86 TYR 0.004 0.001 TYR B 123 PHE 0.012 0.001 PHE B 401 TRP 0.014 0.001 TRP A 98 HIS 0.001 0.000 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 7122) covalent geometry : angle 0.63855 / 0.32 ( 9572) hydrogen bonds : bond 0.04722 / 3.14 ( 498) hydrogen bonds : angle 4.66741 / 3.36 ( 1488) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.229 Fit side-chains REVERT: A 85 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7182 (t0) REVERT: A 198 LYS cc_start: 0.8561 (ttpt) cc_final: 0.7728 (mmtt) REVERT: A 253 MET cc_start: 0.9048 (mmm) cc_final: 0.8713 (mmm) REVERT: A 489 ASP cc_start: 0.7864 (m-30) cc_final: 0.7565 (m-30) REVERT: B 85 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7188 (t0) REVERT: B 198 LYS cc_start: 0.8562 (ttpt) cc_final: 0.7724 (mmtt) REVERT: B 253 MET cc_start: 0.9024 (mmm) cc_final: 0.8676 (mmm) REVERT: B 489 ASP cc_start: 0.7882 (m-30) cc_final: 0.7581 (m-30) outliers start: 10 outliers final: 4 residues processed: 98 average time/residue: 0.0564 time to fit residues: 8.0226 Evaluate side-chains 88 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 417 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 59 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 77 optimal weight: 0.0370 chunk 40 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 79 optimal weight: 0.1980 chunk 3 optimal weight: 2.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 478 HIS B 158 ASN B 478 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.163605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.146748 restraints weight = 8812.118| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.77 r_work: 0.3755 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7122 Z= 0.112 Angle : 0.548 7.949 9572 Z= 0.274 Chirality : 0.039 0.116 1146 Planarity : 0.004 0.057 1122 Dihedral : 12.933 80.483 1212 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.08 % Allowed : 9.52 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.29), residues: 882 helix: 1.25 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -2.09 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 157 TYR 0.005 0.001 TYR B 123 PHE 0.013 0.001 PHE B 323 TRP 0.010 0.001 TRP A 98 HIS 0.002 0.000 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 7122) covalent geometry : angle 0.54827 / 0.27 ( 9572) hydrogen bonds : bond 0.04212 / 2.82 ( 498) hydrogen bonds : angle 4.27559 / 3.07 ( 1488) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.257 Fit side-chains REVERT: A 85 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7069 (t0) REVERT: A 198 LYS cc_start: 0.8617 (ttpt) cc_final: 0.7699 (mmtt) REVERT: A 253 MET cc_start: 0.9001 (mmm) cc_final: 0.8743 (mmm) REVERT: A 489 ASP cc_start: 0.7839 (m-30) cc_final: 0.7527 (m-30) REVERT: B 85 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7077 (t0) REVERT: B 198 LYS cc_start: 0.8615 (ttpt) cc_final: 0.7693 (mmtt) REVERT: B 253 MET cc_start: 0.8961 (mmm) cc_final: 0.8693 (mmm) REVERT: B 489 ASP cc_start: 0.7845 (m-30) cc_final: 0.7526 (m-30) outliers start: 22 outliers final: 10 residues processed: 110 average time/residue: 0.0492 time to fit residues: 7.8688 Evaluate side-chains 96 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 482 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 65 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 HIS B 478 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.161446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.145062 restraints weight = 8866.699| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.74 r_work: 0.3738 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7122 Z= 0.121 Angle : 0.550 8.315 9572 Z= 0.275 Chirality : 0.039 0.132 1146 Planarity : 0.005 0.059 1122 Dihedral : 12.262 61.305 1212 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.36 % Allowed : 10.36 % Favored : 86.27 % 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: 1.03 (0.29), residues: 882 helix: 1.33 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -1.96 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 414 TYR 0.007 0.001 TYR B 123 PHE 0.013 0.001 PHE B 401 TRP 0.011 0.001 TRP A 98 HIS 0.002 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 7122) covalent geometry : angle 0.55003 / 0.27 ( 9572) hydrogen bonds : bond 0.04045 / 2.68 ( 498) hydrogen bonds : angle 4.18981 / 2.99 ( 1488) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.157 Fit side-chains REVERT: A 85 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7416 (t0) REVERT: A 198 LYS cc_start: 0.8680 (ttpt) cc_final: 0.7709 (mmtt) REVERT: A 324 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8450 (mt) REVERT: A 439 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8184 (mmm) REVERT: A 489 ASP cc_start: 0.7845 (m-30) cc_final: 0.7546 (m-30) REVERT: B 85 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7415 (t0) REVERT: B 198 LYS cc_start: 0.8671 (ttpt) cc_final: 0.7694 (mmtt) REVERT: B 324 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8459 (mt) REVERT: B 439 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8193 (mmm) REVERT: B 489 ASP cc_start: 0.7843 (m-30) cc_final: 0.7541 (m-30) outliers start: 24 outliers final: 12 residues processed: 110 average time/residue: 0.0586 time to fit residues: 9.1170 Evaluate side-chains 97 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 482 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 63 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 HIS B 478 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.160571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.144055 restraints weight = 8897.057| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.75 r_work: 0.3726 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7122 Z= 0.124 Angle : 0.562 8.355 9572 Z= 0.276 Chirality : 0.039 0.124 1146 Planarity : 0.004 0.057 1122 Dihedral : 11.975 60.135 1212 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.80 % Allowed : 11.20 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.29), residues: 882 helix: 1.44 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.79 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.007 0.001 TYR A 123 PHE 0.011 0.001 PHE A 401 TRP 0.010 0.001 TRP B 98 HIS 0.002 0.001 HIS A 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 7122) covalent geometry : angle 0.56173 / 0.28 ( 9572) hydrogen bonds : bond 0.04014 / 2.65 ( 498) hydrogen bonds : angle 4.14053 / 2.96 ( 1488) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.221 Fit side-chains REVERT: A 85 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7459 (t0) REVERT: A 195 LYS cc_start: 0.8099 (mmtp) cc_final: 0.7691 (pttm) REVERT: A 198 LYS cc_start: 0.8669 (ttpt) cc_final: 0.7765 (mmtt) REVERT: A 253 MET cc_start: 0.8747 (mmm) cc_final: 0.8168 (mmm) REVERT: A 324 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8466 (mt) REVERT: A 489 ASP cc_start: 0.7841 (m-30) cc_final: 0.7530 (m-30) REVERT: B 85 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7446 (t0) REVERT: B 195 LYS cc_start: 0.8083 (mmtp) cc_final: 0.7675 (pttm) REVERT: B 198 LYS cc_start: 0.8662 (ttpt) cc_final: 0.7749 (mmtt) REVERT: B 253 MET cc_start: 0.8741 (mmm) cc_final: 0.8217 (mmm) REVERT: B 324 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8469 (mt) REVERT: B 489 ASP cc_start: 0.7841 (m-30) cc_final: 0.7532 (m-30) outliers start: 20 outliers final: 12 residues processed: 100 average time/residue: 0.0469 time to fit residues: 7.0899 Evaluate side-chains 102 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 482 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 0.0050 chunk 81 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 HIS B 478 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.162730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.145534 restraints weight = 9090.688| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.81 r_work: 0.3737 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7122 Z= 0.111 Angle : 0.548 7.924 9572 Z= 0.269 Chirality : 0.038 0.126 1146 Planarity : 0.004 0.056 1122 Dihedral : 11.619 59.831 1212 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.66 % Allowed : 11.90 % Favored : 85.43 % 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: 1.36 (0.29), residues: 882 helix: 1.55 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.70 (0.49), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.008 0.001 TYR A 123 PHE 0.009 0.001 PHE B 401 TRP 0.010 0.001 TRP A 98 HIS 0.002 0.000 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 7122) covalent geometry : angle 0.54850 / 0.27 ( 9572) hydrogen bonds : bond 0.03822 / 2.52 ( 498) hydrogen bonds : angle 4.08419 / 2.93 ( 1488) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.193 Fit side-chains REVERT: A 85 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7439 (t0) REVERT: A 195 LYS cc_start: 0.8133 (mmtp) cc_final: 0.7692 (pttm) REVERT: A 198 LYS cc_start: 0.8595 (ttpt) cc_final: 0.7687 (mmtt) REVERT: A 253 MET cc_start: 0.8780 (mmm) cc_final: 0.8254 (mmm) REVERT: A 324 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8389 (mt) REVERT: A 489 ASP cc_start: 0.7848 (m-30) cc_final: 0.7534 (m-30) REVERT: B 195 LYS cc_start: 0.8112 (mmtp) cc_final: 0.7673 (pttm) REVERT: B 198 LYS cc_start: 0.8589 (ttpt) cc_final: 0.7673 (mmtt) REVERT: B 253 MET cc_start: 0.8759 (mmm) cc_final: 0.8226 (mmm) REVERT: B 324 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8386 (mt) REVERT: B 489 ASP cc_start: 0.7848 (m-30) cc_final: 0.7534 (m-30) outliers start: 19 outliers final: 11 residues processed: 105 average time/residue: 0.0531 time to fit residues: 8.0729 Evaluate side-chains 94 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 482 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 53 optimal weight: 0.2980 chunk 33 optimal weight: 0.0980 chunk 28 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 HIS B 478 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.164372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.147350 restraints weight = 8969.400| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.81 r_work: 0.3761 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7122 Z= 0.106 Angle : 0.542 7.521 9572 Z= 0.266 Chirality : 0.039 0.139 1146 Planarity : 0.004 0.054 1122 Dihedral : 11.173 59.902 1212 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.68 % Allowed : 13.87 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.29), residues: 882 helix: 1.63 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.52 (0.49), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 414 TYR 0.007 0.001 TYR B 123 PHE 0.009 0.001 PHE A 401 TRP 0.009 0.001 TRP A 98 HIS 0.002 0.000 HIS A 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 7122) covalent geometry : angle 0.54151 / 0.27 ( 9572) hydrogen bonds : bond 0.03717 / 2.46 ( 498) hydrogen bonds : angle 4.02948 / 2.89 ( 1488) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.199 Fit side-chains REVERT: A 195 LYS cc_start: 0.8124 (mmtp) cc_final: 0.7604 (pttm) REVERT: A 198 LYS cc_start: 0.8581 (ttpt) cc_final: 0.7678 (mmtt) REVERT: A 253 MET cc_start: 0.8752 (mmm) cc_final: 0.8264 (mmm) REVERT: A 324 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8352 (mt) REVERT: A 489 ASP cc_start: 0.7809 (m-30) cc_final: 0.7490 (m-30) REVERT: B 195 LYS cc_start: 0.8118 (mmtp) cc_final: 0.7601 (pttm) REVERT: B 198 LYS cc_start: 0.8587 (ttpt) cc_final: 0.7676 (mmtt) REVERT: B 253 MET cc_start: 0.8738 (mmm) cc_final: 0.8242 (mmm) REVERT: B 324 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8362 (mt) REVERT: B 489 ASP cc_start: 0.7815 (m-30) cc_final: 0.7495 (m-30) outliers start: 12 outliers final: 9 residues processed: 114 average time/residue: 0.0570 time to fit residues: 9.1611 Evaluate side-chains 105 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 482 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 66 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 55 optimal weight: 0.0970 chunk 25 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 HIS B 478 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.163501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.146571 restraints weight = 9051.331| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.82 r_work: 0.3747 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7122 Z= 0.111 Angle : 0.546 7.659 9572 Z= 0.266 Chirality : 0.039 0.131 1146 Planarity : 0.004 0.048 1122 Dihedral : 11.027 59.984 1212 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.10 % Allowed : 13.03 % Favored : 84.87 % 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: 1.50 (0.29), residues: 882 helix: 1.65 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -1.50 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 414 TYR 0.007 0.001 TYR B 123 PHE 0.009 0.001 PHE B 401 TRP 0.009 0.001 TRP A 98 HIS 0.002 0.000 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 7122) covalent geometry : angle 0.54583 / 0.27 ( 9572) hydrogen bonds : bond 0.03752 / 2.48 ( 498) hydrogen bonds : angle 4.03362 / 2.90 ( 1488) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.174 Fit side-chains REVERT: A 195 LYS cc_start: 0.8160 (mmtp) cc_final: 0.7572 (pttm) REVERT: A 198 LYS cc_start: 0.8584 (ttpt) cc_final: 0.7692 (mmtt) REVERT: A 253 MET cc_start: 0.8751 (mmm) cc_final: 0.8250 (mmm) REVERT: A 324 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8382 (mt) REVERT: A 489 ASP cc_start: 0.7825 (m-30) cc_final: 0.7517 (m-30) REVERT: B 195 LYS cc_start: 0.8143 (mmtp) cc_final: 0.7547 (pttm) REVERT: B 198 LYS cc_start: 0.8577 (ttpt) cc_final: 0.7673 (mmtt) REVERT: B 253 MET cc_start: 0.8737 (mmm) cc_final: 0.8224 (mmm) REVERT: B 324 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8406 (mt) REVERT: B 489 ASP cc_start: 0.7825 (m-30) cc_final: 0.7515 (m-30) outliers start: 15 outliers final: 9 residues processed: 108 average time/residue: 0.0544 time to fit residues: 8.5890 Evaluate side-chains 105 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 482 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 28 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 5 optimal weight: 0.0010 chunk 11 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 17 optimal weight: 0.0000 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN A 478 HIS B 325 GLN B 478 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.164597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.147694 restraints weight = 8994.121| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.82 r_work: 0.3764 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7122 Z= 0.104 Angle : 0.535 7.246 9572 Z= 0.262 Chirality : 0.039 0.135 1146 Planarity : 0.004 0.045 1122 Dihedral : 10.841 59.610 1212 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.82 % Allowed : 13.31 % Favored : 84.87 % 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: 1.62 (0.29), residues: 882 helix: 1.71 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -1.33 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 414 TYR 0.007 0.001 TYR B 123 PHE 0.009 0.001 PHE A 401 TRP 0.009 0.001 TRP B 98 HIS 0.002 0.000 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 7122) covalent geometry : angle 0.53472 / 0.26 ( 9572) hydrogen bonds : bond 0.03620 / 2.40 ( 498) hydrogen bonds : angle 4.00356 / 2.88 ( 1488) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.153 Fit side-chains REVERT: A 195 LYS cc_start: 0.8146 (mmtp) cc_final: 0.7564 (pttm) REVERT: A 198 LYS cc_start: 0.8586 (ttpt) cc_final: 0.7696 (mmtt) REVERT: A 253 MET cc_start: 0.8711 (mmm) cc_final: 0.8211 (mmm) REVERT: A 324 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8349 (mt) REVERT: A 489 ASP cc_start: 0.7795 (m-30) cc_final: 0.7497 (m-30) REVERT: B 195 LYS cc_start: 0.8130 (mmtp) cc_final: 0.7539 (pttm) REVERT: B 198 LYS cc_start: 0.8579 (ttpt) cc_final: 0.7679 (mmtt) REVERT: B 253 MET cc_start: 0.8677 (mmm) cc_final: 0.8107 (mmm) REVERT: B 489 ASP cc_start: 0.7803 (m-30) cc_final: 0.7507 (m-30) outliers start: 13 outliers final: 8 residues processed: 105 average time/residue: 0.0581 time to fit residues: 8.9649 Evaluate side-chains 103 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 422 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 0 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 HIS B 478 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.161268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.144174 restraints weight = 9077.221| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.82 r_work: 0.3718 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7122 Z= 0.137 Angle : 0.577 8.195 9572 Z= 0.284 Chirality : 0.040 0.127 1146 Planarity : 0.004 0.047 1122 Dihedral : 11.123 59.121 1212 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.40 % Allowed : 13.45 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.29), residues: 882 helix: 1.55 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -1.40 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 86 TYR 0.009 0.001 TYR B 123 PHE 0.012 0.001 PHE B 401 TRP 0.011 0.001 TRP A 233 HIS 0.003 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 7122) covalent geometry : angle 0.57683 / 0.28 ( 9572) hydrogen bonds : bond 0.04040 / 2.68 ( 498) hydrogen bonds : angle 4.10569 / 2.94 ( 1488) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.154 Fit side-chains REVERT: A 198 LYS cc_start: 0.8585 (ttpt) cc_final: 0.7712 (mmtt) REVERT: A 253 MET cc_start: 0.8772 (mmm) cc_final: 0.8342 (mmm) REVERT: A 324 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8413 (mt) REVERT: A 489 ASP cc_start: 0.7934 (m-30) cc_final: 0.7638 (m-30) REVERT: B 198 LYS cc_start: 0.8590 (ttpt) cc_final: 0.7708 (mmtt) REVERT: B 253 MET cc_start: 0.8747 (mmm) cc_final: 0.8310 (mmm) REVERT: B 324 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8410 (mt) REVERT: B 489 ASP cc_start: 0.7941 (m-30) cc_final: 0.7644 (m-30) outliers start: 10 outliers final: 8 residues processed: 99 average time/residue: 0.0541 time to fit residues: 7.7954 Evaluate side-chains 99 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 422 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 GLN A 478 HIS B 325 GLN B 478 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.162281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.145310 restraints weight = 8978.036| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.80 r_work: 0.3735 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7122 Z= 0.121 Angle : 0.556 7.906 9572 Z= 0.273 Chirality : 0.039 0.129 1146 Planarity : 0.004 0.044 1122 Dihedral : 11.085 59.238 1212 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.40 % Allowed : 13.73 % Favored : 84.87 % 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: 1.48 (0.29), residues: 882 helix: 1.60 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -1.34 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.007 0.001 TYR B 123 PHE 0.010 0.001 PHE A 495 TRP 0.009 0.001 TRP B 98 HIS 0.002 0.001 HIS A 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 7122) covalent geometry : angle 0.55555 / 0.27 ( 9572) hydrogen bonds : bond 0.03835 / 2.54 ( 498) hydrogen bonds : angle 4.06850 / 2.92 ( 1488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1426.84 seconds wall clock time: 25 minutes 7.97 seconds (1507.97 seconds total)