Starting phenix.real_space_refine on Wed Aug 5 02:54:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w6d_37321/08_2026/8w6d_37321.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w6d_37321/08_2026/8w6d_37321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w6d_37321/08_2026/8w6d_37321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w6d_37321/08_2026/8w6d_37321.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w6d_37321/08_2026/8w6d_37321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w6d_37321/08_2026/8w6d_37321.map" } resolution = 2.5 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= 0.006 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 2 5.49 5 S 56 5.16 5 Na 2 4.78 5 C 5566 2.51 5 N 1286 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8304 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4068 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 495} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {' NA': 1, '3PH': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 3.36, per 1000 atoms: 0.40 Number of scatterers: 8304 At special positions: 0 Unit cell: (88.047, 107.613, 89.134, 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 56 16.00 P 2 15.00 Na 2 11.00 O 1392 8.00 N 1286 7.00 C 5566 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: 0.65 Conformation dependent library (CDL) restraints added in 218.9 milliseconds 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 2 sheets defined 77.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.725A pdb=" N LEU A 8 " --> pdb=" O CYS A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 24 Proline residue: A 21 - end of helix Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 33 through 52 Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 62 through 70 Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.667A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 103 removed outlier: 3.567A pdb=" N VAL A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 118 removed outlier: 3.781A pdb=" N ARG A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 136 Processing helix chain 'A' and resid 140 through 163 Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 214 through 232 removed outlier: 3.661A pdb=" N SER A 230 " --> pdb=" O CYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 240 through 254 removed outlier: 3.969A pdb=" N LEU A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 290 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 305 through 322 removed outlier: 3.695A pdb=" N GLN A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 346 removed outlier: 3.512A pdb=" N THR A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 369 through 384 removed outlier: 3.933A pdb=" N PHE A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 418 through 438 removed outlier: 3.641A pdb=" N VAL A 422 " --> pdb=" O PRO A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 447 through 453 Proline residue: A 450 - end of helix removed outlier: 4.309A pdb=" N SER A 453 " --> pdb=" O PRO A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 447 through 453' Processing helix chain 'A' and resid 455 through 474 removed outlier: 3.625A pdb=" N ALA A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 461 " --> pdb=" O PRO A 457 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS A 473 " --> pdb=" O THR A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 494 removed outlier: 3.655A pdb=" N LEU A 484 " --> pdb=" O THR A 480 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 3.523A pdb=" N ILE A 494 " --> pdb=" O MET A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 509 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.519A pdb=" N VAL A 525 " --> pdb=" O PRO A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 556 removed outlier: 3.540A pdb=" N MET A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A 545 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.621A pdb=" N GLN A 573 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 removed outlier: 3.726A pdb=" N LEU B 8 " --> pdb=" O CYS B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 24 Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 25 through 31 Processing helix chain 'B' and resid 33 through 52 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 62 through 70 Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.667A pdb=" N VAL B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 103 removed outlier: 3.567A pdb=" N VAL B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.781A pdb=" N ARG B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 136 Processing helix chain 'B' and resid 140 through 163 Proline residue: B 150 - end of helix Processing helix chain 'B' and resid 214 through 232 removed outlier: 3.660A pdb=" N SER B 230 " --> pdb=" O CYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 240 through 254 removed outlier: 3.968A pdb=" N LEU B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 290 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.695A pdb=" N GLN B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B 310 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 346 removed outlier: 3.512A pdb=" N THR B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 369 through 384 removed outlier: 3.934A pdb=" N PHE B 382 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE B 383 " --> pdb=" O ILE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 418 through 438 removed outlier: 3.641A pdb=" N VAL B 422 " --> pdb=" O PRO B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 446 Processing helix chain 'B' and resid 447 through 453 Proline residue: B 450 - end of helix removed outlier: 4.309A pdb=" N SER B 453 " --> pdb=" O PRO B 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 447 through 453' Processing helix chain 'B' and resid 455 through 474 removed outlier: 3.625A pdb=" N ALA B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 461 " --> pdb=" O PRO B 457 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 494 removed outlier: 3.656A pdb=" N LEU B 484 " --> pdb=" O THR B 480 " (cutoff:3.500A) Proline residue: B 485 - end of helix removed outlier: 3.524A pdb=" N ILE B 494 " --> pdb=" O MET B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 509 Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.519A pdb=" N VAL B 525 " --> pdb=" O PRO B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 556 removed outlier: 3.540A pdb=" N MET B 536 " --> pdb=" O LYS B 532 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU B 542 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 545 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 564 Processing helix chain 'B' and resid 569 through 573 removed outlier: 3.621A pdb=" N GLN B 573 " --> pdb=" O SER B 570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 392 through 393 Processing sheet with id=AA2, first strand: chain 'B' and resid 392 through 393 501 hydrogen bonds defined for protein. 1491 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: 1.26 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1305 1.32 - 1.44: 2218 1.44 - 1.56: 4915 1.56 - 1.69: 2 1.69 - 1.81: 92 Bond restraints: 8532 Sorted by residual: bond pdb=" O11 3PH A 802 " pdb=" P 3PH A 802 " ideal model delta sigma weight residual 1.703 1.611 0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" O11 3PH B 802 " pdb=" P 3PH B 802 " ideal model delta sigma weight residual 1.703 1.612 0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C1 3PH B 802 " pdb=" O11 3PH B 802 " ideal model delta sigma weight residual 1.385 1.451 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C1 3PH A 802 " pdb=" O11 3PH A 802 " ideal model delta sigma weight residual 1.385 1.451 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C PRO B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 1.334 1.369 -0.035 1.51e-02 4.39e+03 5.35e+00 ... (remaining 8527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 11215 2.50 - 5.01: 363 5.01 - 7.51: 62 7.51 - 10.01: 10 10.01 - 12.51: 2 Bond angle restraints: 11652 Sorted by residual: angle pdb=" N PRO A 520 " pdb=" CA PRO A 520 " pdb=" C PRO A 520 " ideal model delta sigma weight residual 110.70 117.59 -6.89 1.22e+00 6.72e-01 3.19e+01 angle pdb=" N PRO B 520 " pdb=" CA PRO B 520 " pdb=" C PRO B 520 " ideal model delta sigma weight residual 110.70 117.57 -6.87 1.22e+00 6.72e-01 3.17e+01 angle pdb=" CA THR A 519 " pdb=" CB THR A 519 " pdb=" CG2 THR A 519 " ideal model delta sigma weight residual 110.50 118.13 -7.63 1.70e+00 3.46e-01 2.02e+01 angle pdb=" CA THR B 519 " pdb=" CB THR B 519 " pdb=" CG2 THR B 519 " ideal model delta sigma weight residual 110.50 118.10 -7.60 1.70e+00 3.46e-01 2.00e+01 angle pdb=" C SER A 557 " pdb=" N TRP A 558 " pdb=" CA TRP A 558 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 ... (remaining 11647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 4628 17.13 - 34.25: 362 34.25 - 51.38: 80 51.38 - 68.51: 10 68.51 - 85.63: 8 Dihedral angle restraints: 5088 sinusoidal: 2032 harmonic: 3056 Sorted by residual: dihedral pdb=" CA GLU A 302 " pdb=" C GLU A 302 " pdb=" N LYS A 303 " pdb=" CA LYS A 303 " ideal model delta harmonic sigma weight residual 180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU B 302 " pdb=" C GLU B 302 " pdb=" N LYS B 303 " pdb=" CA LYS B 303 " ideal model delta harmonic sigma weight residual 180.00 -159.91 -20.09 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ALA B 512 " pdb=" C ALA B 512 " pdb=" N PHE B 513 " pdb=" CA PHE B 513 " ideal model delta harmonic sigma weight residual -180.00 -160.97 -19.03 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 5085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1049 0.062 - 0.124: 276 0.124 - 0.185: 52 0.185 - 0.247: 11 0.247 - 0.309: 4 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CA THR A 519 " pdb=" N THR A 519 " pdb=" C THR A 519 " pdb=" CB THR A 519 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA THR B 519 " pdb=" N THR B 519 " pdb=" C THR B 519 " pdb=" CB THR B 519 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CBE Y01 A 803 " pdb=" CAP Y01 A 803 " pdb=" CBB Y01 A 803 " pdb=" CBI Y01 A 803 " both_signs ideal model delta sigma weight residual False 2.57 2.32 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1389 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 25 " -0.045 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO B 26 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 26 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 26 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 25 " 0.045 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO A 26 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 67 " -0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO A 68 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " -0.038 5.00e-02 4.00e+02 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 2962 2.89 - 3.39: 8074 3.39 - 3.90: 13776 3.90 - 4.40: 15511 4.40 - 4.90: 26347 Nonbonded interactions: 66670 Sorted by model distance: nonbonded pdb=" O VAL A 467 " pdb=" OG1 THR A 471 " model vdw 2.391 3.040 nonbonded pdb=" O VAL B 467 " pdb=" OG1 THR B 471 " model vdw 2.392 3.040 nonbonded pdb=" OG SER B 33 " pdb=" OE1 GLU B 35 " model vdw 2.414 3.040 nonbonded pdb=" OG SER A 33 " pdb=" OE1 GLU A 35 " model vdw 2.415 3.040 nonbonded pdb=" O TRP A 9 " pdb=" NH1 ARG A 12 " model vdw 2.422 3.120 ... (remaining 66665 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.600 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.410 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 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 : 0.009 0.092 8532 Z= 0.371 Angle : 1.076 12.515 11652 Z= 0.580 Chirality : 0.062 0.309 1392 Planarity : 0.009 0.067 1402 Dihedral : 13.435 85.633 3104 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.95 % Favored : 94.86 % Rotamer: Outliers : 0.23 % Allowed : 2.85 % Favored : 96.92 % 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: -2.77 (0.22), residues: 1050 helix: -1.06 (0.16), residues: 726 sheet: -4.33 (0.46), residues: 20 loop : -3.36 (0.30), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 112 TYR 0.011 0.002 TYR A 500 PHE 0.043 0.003 PHE B 344 TRP 0.037 0.003 TRP A 410 HIS 0.008 0.002 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00911 / 0.37 ( 8532) covalent geometry : angle 1.07574 / 0.58 (11652) hydrogen bonds : bond 0.17338 / 11.29 ( 501) hydrogen bonds : angle 5.43743 / 3.75 ( 1491) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.278 Fit side-chains REVERT: A 70 MET cc_start: 0.8160 (mtm) cc_final: 0.7951 (mtp) REVERT: A 137 MET cc_start: 0.8884 (mtp) cc_final: 0.8647 (mtp) REVERT: A 303 LYS cc_start: 0.7143 (tttm) cc_final: 0.6850 (tttp) REVERT: A 318 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7399 (tp30) REVERT: A 344 PHE cc_start: 0.7876 (m-80) cc_final: 0.7605 (t80) REVERT: A 417 MET cc_start: 0.9113 (tpp) cc_final: 0.8862 (tpp) REVERT: A 490 MET cc_start: 0.8214 (tmm) cc_final: 0.7771 (tmm) REVERT: B 70 MET cc_start: 0.8159 (mtm) cc_final: 0.7922 (mtp) REVERT: B 137 MET cc_start: 0.8883 (mtp) cc_final: 0.8651 (mtp) REVERT: B 303 LYS cc_start: 0.7134 (tttm) cc_final: 0.6840 (tttp) REVERT: B 318 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7406 (tp30) REVERT: B 344 PHE cc_start: 0.7877 (m-80) cc_final: 0.7606 (t80) REVERT: B 417 MET cc_start: 0.9113 (tpp) cc_final: 0.8870 (tpp) REVERT: B 490 MET cc_start: 0.8214 (tmm) cc_final: 0.7769 (tmm) outliers start: 2 outliers final: 2 residues processed: 126 average time/residue: 0.6503 time to fit residues: 85.9765 Evaluate side-chains 100 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 517 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN A 243 ASN A 257 ASN A 297 ASN A 305 GLN A 356 ASN A 397 ASN A 414 ASN B 243 ASN B 257 ASN B 297 ASN B 305 GLN B 356 ASN B 397 ASN B 414 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.093396 restraints weight = 9595.899| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.41 r_work: 0.2865 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8532 Z= 0.132 Angle : 0.613 7.436 11652 Z= 0.316 Chirality : 0.042 0.163 1392 Planarity : 0.006 0.057 1402 Dihedral : 8.726 53.373 1304 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.37 % Allowed : 8.33 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.26), residues: 1050 helix: 0.96 (0.19), residues: 750 sheet: -4.19 (0.48), residues: 20 loop : -2.89 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 295 TYR 0.005 0.001 TYR B 11 PHE 0.014 0.001 PHE A 344 TRP 0.023 0.002 TRP B 558 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 8532) covalent geometry : angle 0.61286 / 0.32 (11652) hydrogen bonds : bond 0.05312 / 3.55 ( 501) hydrogen bonds : angle 3.95102 / 2.72 ( 1491) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.284 Fit side-chains REVERT: A 163 GLN cc_start: 0.7679 (mt0) cc_final: 0.7403 (mt0) REVERT: A 303 LYS cc_start: 0.7223 (tttm) cc_final: 0.6462 (ttpp) REVERT: A 304 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7478 (mmt) REVERT: A 318 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7983 (tp30) REVERT: A 325 MET cc_start: 0.9093 (mtp) cc_final: 0.8873 (mtp) REVERT: A 490 MET cc_start: 0.8597 (tmm) cc_final: 0.8192 (tmm) REVERT: B 52 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7900 (tp30) REVERT: B 163 GLN cc_start: 0.7686 (mt0) cc_final: 0.7414 (mt0) REVERT: B 303 LYS cc_start: 0.7217 (tttm) cc_final: 0.6463 (ttpp) REVERT: B 304 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7476 (mmt) REVERT: B 318 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7973 (tp30) REVERT: B 325 MET cc_start: 0.9093 (mtp) cc_final: 0.8874 (mtp) REVERT: B 490 MET cc_start: 0.8647 (tmm) cc_final: 0.8257 (tmm) outliers start: 12 outliers final: 4 residues processed: 113 average time/residue: 0.5414 time to fit residues: 64.8512 Evaluate side-chains 103 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 517 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 31 optimal weight: 0.3980 chunk 83 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.118321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.094496 restraints weight = 9484.616| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.41 r_work: 0.2898 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8532 Z= 0.122 Angle : 0.582 7.345 11652 Z= 0.298 Chirality : 0.042 0.166 1392 Planarity : 0.005 0.057 1402 Dihedral : 8.424 54.226 1304 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.28 % Allowed : 7.99 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.27), residues: 1050 helix: 1.84 (0.19), residues: 748 sheet: -4.11 (0.52), residues: 20 loop : -2.70 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 320 TYR 0.005 0.001 TYR B 40 PHE 0.011 0.001 PHE B 351 TRP 0.020 0.002 TRP A 410 HIS 0.002 0.001 HIS B 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 8532) covalent geometry : angle 0.58173 / 0.30 (11652) hydrogen bonds : bond 0.04723 / 3.16 ( 501) hydrogen bonds : angle 3.66515 / 2.53 ( 1491) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.349 Fit side-chains REVERT: A 70 MET cc_start: 0.8746 (mtm) cc_final: 0.8393 (mtp) REVERT: A 85 ASP cc_start: 0.8104 (t70) cc_final: 0.7898 (t70) REVERT: A 163 GLN cc_start: 0.7597 (mt0) cc_final: 0.7298 (mt0) REVERT: A 303 LYS cc_start: 0.7214 (tttm) cc_final: 0.6791 (tttp) REVERT: A 304 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7445 (mmt) REVERT: A 318 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7997 (tp30) REVERT: A 490 MET cc_start: 0.8597 (tmm) cc_final: 0.8347 (tmm) REVERT: B 70 MET cc_start: 0.8741 (mtm) cc_final: 0.8388 (mtp) REVERT: B 85 ASP cc_start: 0.8114 (t70) cc_final: 0.7902 (t70) REVERT: B 163 GLN cc_start: 0.7599 (mt0) cc_final: 0.7304 (mt0) REVERT: B 303 LYS cc_start: 0.7211 (tttm) cc_final: 0.6796 (tttp) REVERT: B 304 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7441 (mmt) REVERT: B 318 GLU cc_start: 0.8208 (mm-30) cc_final: 0.8004 (tp30) REVERT: B 490 MET cc_start: 0.8601 (tmm) cc_final: 0.8351 (tmm) outliers start: 20 outliers final: 5 residues processed: 112 average time/residue: 0.5675 time to fit residues: 67.2302 Evaluate side-chains 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 517 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 81 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 65 optimal weight: 0.0270 chunk 47 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 98 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.4444 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.115868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.092088 restraints weight = 9751.797| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.38 r_work: 0.2836 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8532 Z= 0.156 Angle : 0.656 10.147 11652 Z= 0.328 Chirality : 0.044 0.172 1392 Planarity : 0.006 0.060 1402 Dihedral : 8.799 54.828 1304 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.28 % Allowed : 9.02 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.28), residues: 1050 helix: 1.91 (0.20), residues: 758 sheet: -4.02 (0.54), residues: 20 loop : -2.34 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 346 TYR 0.010 0.001 TYR B 500 PHE 0.017 0.002 PHE B 568 TRP 0.023 0.002 TRP B 410 HIS 0.003 0.001 HIS B 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 8532) covalent geometry : angle 0.65559 / 0.33 (11652) hydrogen bonds : bond 0.06002 / 3.99 ( 501) hydrogen bonds : angle 3.74023 / 2.60 ( 1491) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.313 Fit side-chains REVERT: A 163 GLN cc_start: 0.7630 (mt0) cc_final: 0.7284 (mt0) REVERT: A 295 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7772 (mtp180) REVERT: A 303 LYS cc_start: 0.7022 (tttm) cc_final: 0.6642 (tttp) REVERT: A 318 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7884 (tp30) REVERT: A 490 MET cc_start: 0.8614 (tmm) cc_final: 0.8400 (tmm) REVERT: B 85 ASP cc_start: 0.8184 (t70) cc_final: 0.7980 (t70) REVERT: B 163 GLN cc_start: 0.7637 (mt0) cc_final: 0.7298 (mt0) REVERT: B 295 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7761 (mtp180) REVERT: B 303 LYS cc_start: 0.7028 (tttm) cc_final: 0.6653 (tttp) REVERT: B 318 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7876 (tp30) REVERT: B 490 MET cc_start: 0.8624 (tmm) cc_final: 0.8412 (tmm) outliers start: 20 outliers final: 11 residues processed: 112 average time/residue: 0.4892 time to fit residues: 58.2438 Evaluate side-chains 113 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 558 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 54 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 59 optimal weight: 0.0870 chunk 31 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.092882 restraints weight = 9678.668| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.38 r_work: 0.2863 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8532 Z= 0.137 Angle : 0.618 8.413 11652 Z= 0.312 Chirality : 0.044 0.228 1392 Planarity : 0.005 0.060 1402 Dihedral : 8.801 54.269 1304 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.05 % Allowed : 9.70 % Favored : 88.24 % 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: 1.31 (0.28), residues: 1050 helix: 2.05 (0.19), residues: 760 sheet: -3.87 (0.60), residues: 20 loop : -2.33 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 437 TYR 0.007 0.001 TYR B 500 PHE 0.015 0.001 PHE A 568 TRP 0.023 0.002 TRP A 410 HIS 0.002 0.001 HIS B 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 8532) covalent geometry : angle 0.61830 / 0.31 (11652) hydrogen bonds : bond 0.05328 / 3.56 ( 501) hydrogen bonds : angle 3.66073 / 2.54 ( 1491) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.211 Fit side-chains REVERT: A 70 MET cc_start: 0.8783 (mtm) cc_final: 0.8428 (mtp) REVERT: A 163 GLN cc_start: 0.7572 (mt0) cc_final: 0.7327 (mt0) REVERT: A 303 LYS cc_start: 0.6958 (tttm) cc_final: 0.6566 (tttp) REVERT: A 490 MET cc_start: 0.8601 (tmm) cc_final: 0.8391 (tmm) REVERT: B 70 MET cc_start: 0.8790 (mtm) cc_final: 0.8434 (mtp) REVERT: B 163 GLN cc_start: 0.7564 (mt0) cc_final: 0.7326 (mt0) REVERT: B 295 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7490 (mtp85) REVERT: B 303 LYS cc_start: 0.6957 (tttm) cc_final: 0.6574 (tttp) REVERT: B 304 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7451 (mmt) REVERT: B 490 MET cc_start: 0.8610 (tmm) cc_final: 0.8403 (tmm) outliers start: 18 outliers final: 10 residues processed: 111 average time/residue: 0.5505 time to fit residues: 64.8421 Evaluate side-chains 114 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 558 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 101 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 3 optimal weight: 0.0870 chunk 95 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.092018 restraints weight = 9539.210| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.37 r_work: 0.2838 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8532 Z= 0.151 Angle : 0.643 8.802 11652 Z= 0.323 Chirality : 0.044 0.212 1392 Planarity : 0.005 0.060 1402 Dihedral : 9.075 55.014 1304 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.17 % Allowed : 9.47 % Favored : 88.36 % 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: 1.38 (0.28), residues: 1050 helix: 2.06 (0.19), residues: 758 sheet: -3.73 (0.64), residues: 20 loop : -2.16 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.009 0.001 TYR B 500 PHE 0.016 0.002 PHE B 568 TRP 0.024 0.002 TRP A 410 HIS 0.003 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 8532) covalent geometry : angle 0.64252 / 0.32 (11652) hydrogen bonds : bond 0.05784 / 3.85 ( 501) hydrogen bonds : angle 3.69056 / 2.57 ( 1491) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.272 Fit side-chains REVERT: A 18 PHE cc_start: 0.8353 (t80) cc_final: 0.7697 (m-80) REVERT: A 163 GLN cc_start: 0.7578 (mt0) cc_final: 0.7250 (mt0) REVERT: A 295 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7713 (mtp180) REVERT: A 303 LYS cc_start: 0.6953 (tttm) cc_final: 0.6568 (tttp) REVERT: A 304 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7465 (mmt) REVERT: B 18 PHE cc_start: 0.8331 (t80) cc_final: 0.7693 (m-80) REVERT: B 163 GLN cc_start: 0.7584 (mt0) cc_final: 0.7310 (mt0) REVERT: B 295 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7768 (mtp180) REVERT: B 303 LYS cc_start: 0.6944 (tttm) cc_final: 0.6555 (tttp) outliers start: 19 outliers final: 10 residues processed: 106 average time/residue: 0.5028 time to fit residues: 56.5609 Evaluate side-chains 110 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 558 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 81 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.112650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.088419 restraints weight = 9681.093| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.41 r_work: 0.2782 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8532 Z= 0.240 Angle : 0.769 10.024 11652 Z= 0.386 Chirality : 0.050 0.224 1392 Planarity : 0.006 0.059 1402 Dihedral : 10.097 59.190 1304 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.19 % Favored : 95.62 % Rotamer: Outliers : 1.71 % Allowed : 9.93 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.27), residues: 1050 helix: 1.58 (0.19), residues: 768 sheet: -3.50 (0.66), residues: 20 loop : -2.18 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 346 TYR 0.013 0.002 TYR A 500 PHE 0.024 0.003 PHE A 568 TRP 0.028 0.003 TRP B 410 HIS 0.004 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.24 ( 8532) covalent geometry : angle 0.76924 / 0.39 (11652) hydrogen bonds : bond 0.07812 / 5.18 ( 501) hydrogen bonds : angle 3.94308 / 2.75 ( 1491) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.313 Fit side-chains REVERT: A 18 PHE cc_start: 0.8347 (t80) cc_final: 0.7686 (m-80) REVERT: A 163 GLN cc_start: 0.7704 (mt0) cc_final: 0.7319 (mt0) REVERT: A 295 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7683 (mtp180) REVERT: A 303 LYS cc_start: 0.6914 (tttm) cc_final: 0.6505 (tttp) REVERT: B 18 PHE cc_start: 0.8286 (t80) cc_final: 0.7702 (m-80) REVERT: B 163 GLN cc_start: 0.7716 (mt0) cc_final: 0.7337 (mt0) REVERT: B 295 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7754 (mtp180) REVERT: B 303 LYS cc_start: 0.6981 (tttm) cc_final: 0.6590 (tttp) outliers start: 15 outliers final: 11 residues processed: 104 average time/residue: 0.5753 time to fit residues: 63.5126 Evaluate side-chains 109 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 558 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 51 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.116941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.093446 restraints weight = 9619.412| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.36 r_work: 0.2872 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8532 Z= 0.134 Angle : 0.615 8.093 11652 Z= 0.312 Chirality : 0.043 0.218 1392 Planarity : 0.005 0.057 1402 Dihedral : 9.571 57.232 1304 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.83 % Allowed : 10.84 % Favored : 87.33 % 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: 1.47 (0.27), residues: 1050 helix: 2.13 (0.19), residues: 758 sheet: -3.52 (0.68), residues: 20 loop : -2.15 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 320 TYR 0.007 0.001 TYR A 40 PHE 0.013 0.001 PHE B 568 TRP 0.024 0.002 TRP B 410 HIS 0.002 0.001 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 8532) covalent geometry : angle 0.61452 / 0.31 (11652) hydrogen bonds : bond 0.05084 / 3.39 ( 501) hydrogen bonds : angle 3.67646 / 2.55 ( 1491) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.348 Fit side-chains REVERT: A 18 PHE cc_start: 0.8269 (t80) cc_final: 0.7684 (m-80) REVERT: A 70 MET cc_start: 0.8811 (mtm) cc_final: 0.8458 (mtp) REVERT: A 163 GLN cc_start: 0.7519 (mt0) cc_final: 0.7195 (mt0) REVERT: A 303 LYS cc_start: 0.6862 (tttm) cc_final: 0.6450 (tttp) REVERT: B 18 PHE cc_start: 0.8238 (t80) cc_final: 0.7666 (m-80) REVERT: B 70 MET cc_start: 0.8761 (mtm) cc_final: 0.8429 (mtp) REVERT: B 163 GLN cc_start: 0.7528 (mt0) cc_final: 0.7212 (mt0) REVERT: B 303 LYS cc_start: 0.6859 (tttm) cc_final: 0.6451 (tttp) outliers start: 16 outliers final: 10 residues processed: 108 average time/residue: 0.5406 time to fit residues: 61.8060 Evaluate side-chains 109 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 558 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 0.4980 chunk 37 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 20 optimal weight: 0.0270 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN A 393 GLN B 286 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.119469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.096140 restraints weight = 9698.317| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.37 r_work: 0.2892 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8532 Z= 0.122 Angle : 0.582 7.799 11652 Z= 0.295 Chirality : 0.042 0.225 1392 Planarity : 0.005 0.057 1402 Dihedral : 9.164 55.002 1304 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.71 % Allowed : 11.42 % Favored : 86.87 % 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: 1.70 (0.28), residues: 1050 helix: 2.37 (0.20), residues: 756 sheet: -3.45 (0.69), residues: 20 loop : -2.25 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 320 TYR 0.007 0.001 TYR A 40 PHE 0.011 0.001 PHE A 351 TRP 0.023 0.002 TRP B 410 HIS 0.004 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 8532) covalent geometry : angle 0.58192 / 0.29 (11652) hydrogen bonds : bond 0.04292 / 2.86 ( 501) hydrogen bonds : angle 3.53779 / 2.45 ( 1491) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.312 Fit side-chains REVERT: A 18 PHE cc_start: 0.8183 (t80) cc_final: 0.7634 (m-80) REVERT: A 70 MET cc_start: 0.8775 (mtm) cc_final: 0.8437 (mtp) REVERT: A 163 GLN cc_start: 0.7489 (mt0) cc_final: 0.7253 (mt0) REVERT: A 256 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6911 (pm20) REVERT: A 303 LYS cc_start: 0.6856 (tttm) cc_final: 0.6455 (tttp) REVERT: B 18 PHE cc_start: 0.8159 (t80) cc_final: 0.7586 (m-80) REVERT: B 70 MET cc_start: 0.8775 (mtm) cc_final: 0.8445 (mtp) REVERT: B 163 GLN cc_start: 0.7491 (mt0) cc_final: 0.7261 (mt0) REVERT: B 256 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6926 (pm20) REVERT: B 303 LYS cc_start: 0.6852 (tttm) cc_final: 0.6451 (tttp) outliers start: 15 outliers final: 5 residues processed: 108 average time/residue: 0.5693 time to fit residues: 65.0584 Evaluate side-chains 101 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 517 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 20 optimal weight: 0.3980 chunk 5 optimal weight: 0.0470 chunk 94 optimal weight: 0.0570 chunk 86 optimal weight: 0.0370 chunk 35 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 overall best weight: 0.2274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.100689 restraints weight = 9683.353| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.37 r_work: 0.2993 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8532 Z= 0.111 Angle : 0.557 7.066 11652 Z= 0.282 Chirality : 0.041 0.260 1392 Planarity : 0.005 0.058 1402 Dihedral : 8.611 51.770 1304 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.57 % Allowed : 12.67 % Favored : 86.76 % 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: 1.98 (0.28), residues: 1050 helix: 2.58 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -2.19 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 320 TYR 0.007 0.001 TYR A 429 PHE 0.012 0.001 PHE B 376 TRP 0.020 0.001 TRP A 410 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 8532) covalent geometry : angle 0.55688 / 0.28 (11652) hydrogen bonds : bond 0.03252 / 2.17 ( 501) hydrogen bonds : angle 3.41390 / 2.36 ( 1491) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.214 Fit side-chains REVERT: A 18 PHE cc_start: 0.8135 (t80) cc_final: 0.7551 (m-80) REVERT: A 70 MET cc_start: 0.8721 (mtm) cc_final: 0.8449 (mtp) REVERT: A 160 HIS cc_start: 0.7782 (m-70) cc_final: 0.7515 (m90) REVERT: A 303 LYS cc_start: 0.6803 (tttm) cc_final: 0.6411 (tttp) REVERT: B 18 PHE cc_start: 0.8108 (t80) cc_final: 0.7539 (m-80) REVERT: B 70 MET cc_start: 0.8735 (mtm) cc_final: 0.8433 (mtp) REVERT: B 160 HIS cc_start: 0.7802 (m-70) cc_final: 0.7519 (m90) REVERT: B 303 LYS cc_start: 0.6788 (tttm) cc_final: 0.6401 (tttp) outliers start: 5 outliers final: 4 residues processed: 107 average time/residue: 0.4932 time to fit residues: 56.1916 Evaluate side-chains 102 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 517 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 286 GLN A 446 ASN B 163 GLN B 393 GLN B 446 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.092974 restraints weight = 9557.222| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.37 r_work: 0.2848 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8532 Z= 0.161 Angle : 0.650 8.654 11652 Z= 0.329 Chirality : 0.045 0.216 1392 Planarity : 0.006 0.060 1402 Dihedral : 9.255 55.484 1304 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.26 % Allowed : 11.64 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.28), residues: 1050 helix: 2.22 (0.20), residues: 760 sheet: -3.31 (0.73), residues: 20 loop : -2.03 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.010 0.001 TYR B 500 PHE 0.017 0.002 PHE A 568 TRP 0.023 0.002 TRP B 410 HIS 0.005 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 8532) covalent geometry : angle 0.65013 / 0.33 (11652) hydrogen bonds : bond 0.05881 / 3.92 ( 501) hydrogen bonds : angle 3.60858 / 2.52 ( 1491) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2799.79 seconds wall clock time: 48 minutes 9.94 seconds (2889.94 seconds total)