Starting phenix.real_space_refine on Thu Jul 2 10:21:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w6d_37321/07_2026/8w6d_37321.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w6d_37321/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8w6d_37321/07_2026/8w6d_37321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w6d_37321/07_2026/8w6d_37321.map" model { file = "/net/cci-nas-00/data/ceres_data/8w6d_37321/07_2026/8w6d_37321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w6d_37321/07_2026/8w6d_37321.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 83 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'3PH': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 2.75, per 1000 atoms: 0.33 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: 0.56 Conformation dependent library (CDL) restraints added in 306.7 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: 0.22 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: 1.31 Time building geometry restraints manager: 0.70 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: 0.910 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.830 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: 0.010 Load rotamer database and sin/cos tables:7.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.690 ------------------------------------------------------------------------------- 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 : 0.178 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: 0.5669 time to fit residues: 75.0805 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 : 0.211 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.116431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.092318 restraints weight = 9590.262| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.42 r_work: 0.2851 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1346 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= 0.135 Angle : 0.633 7.733 11652 Z= 0.328 Chirality : 0.042 0.174 1392 Planarity : 0.006 0.058 1402 Dihedral : 8.729 51.661 1304 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.14 % Allowed : 8.79 % Favored : 90.07 % 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: -0.25 (0.26), residues: 1050 helix: 0.93 (0.19), residues: 746 sheet: -4.21 (0.48), residues: 20 loop : -2.84 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 112 TYR 0.004 0.001 TYR B 500 PHE 0.014 0.001 PHE B 344 TRP 0.025 0.002 TRP B 558 HIS 0.002 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 ( 8532) covalent geometry : angle 0.63264 / 0.33 (11652) hydrogen bonds : bond 0.05630 / 3.77 ( 501) hydrogen bonds : angle 3.99069 / 2.74 ( 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 117 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.268 Fit side-chains REVERT: A 163 GLN cc_start: 0.7865 (mt0) cc_final: 0.7584 (mt0) REVERT: A 303 LYS cc_start: 0.7239 (tttm) cc_final: 0.6461 (ttpp) REVERT: A 318 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7983 (tp30) REVERT: A 325 MET cc_start: 0.9106 (mtp) cc_final: 0.8899 (mtp) REVERT: A 490 MET cc_start: 0.8646 (tmm) cc_final: 0.8267 (tmm) REVERT: B 52 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7821 (tp30) REVERT: B 163 GLN cc_start: 0.7871 (mt0) cc_final: 0.7593 (mt0) REVERT: B 303 LYS cc_start: 0.7233 (tttm) cc_final: 0.6461 (ttpp) REVERT: B 318 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7974 (tp30) REVERT: B 325 MET cc_start: 0.9107 (mtp) cc_final: 0.8901 (mtp) REVERT: B 490 MET cc_start: 0.8655 (tmm) cc_final: 0.8278 (tmm) outliers start: 10 outliers final: 4 residues processed: 113 average time/residue: 0.5038 time to fit residues: 60.3552 Evaluate side-chains 99 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 256 GLN 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: 4.9990 chunk 38 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 86 optimal weight: 0.0050 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN B 286 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.096816 restraints weight = 9495.493| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.34 r_work: 0.2914 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1818 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= 0.119 Angle : 0.572 7.109 11652 Z= 0.293 Chirality : 0.041 0.166 1392 Planarity : 0.005 0.057 1402 Dihedral : 8.344 54.468 1304 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.28 % Allowed : 8.79 % Favored : 88.93 % 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: 0.89 (0.27), residues: 1050 helix: 1.86 (0.19), residues: 748 sheet: -4.07 (0.53), residues: 20 loop : -2.69 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.005 0.001 TYR A 40 PHE 0.011 0.001 PHE B 351 TRP 0.018 0.001 TRP A 410 HIS 0.002 0.000 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 8532) covalent geometry : angle 0.57170 / 0.29 (11652) hydrogen bonds : bond 0.04379 / 2.92 ( 501) hydrogen bonds : angle 3.63136 / 2.51 ( 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 120 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.273 Fit side-chains REVERT: A 70 MET cc_start: 0.8754 (mtm) cc_final: 0.8425 (mtp) REVERT: A 163 GLN cc_start: 0.7531 (mt0) cc_final: 0.7231 (mt0) REVERT: A 303 LYS cc_start: 0.7187 (tttm) cc_final: 0.6758 (tttp) REVERT: A 304 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7445 (mmt) REVERT: A 318 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7998 (tp30) REVERT: A 325 MET cc_start: 0.9093 (mtp) cc_final: 0.8893 (mtp) REVERT: A 490 MET cc_start: 0.8613 (tmm) cc_final: 0.8358 (tmm) REVERT: B 52 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7836 (tp30) REVERT: B 70 MET cc_start: 0.8755 (mtm) cc_final: 0.8425 (mtp) REVERT: B 163 GLN cc_start: 0.7550 (mt0) cc_final: 0.7257 (mt0) REVERT: B 303 LYS cc_start: 0.7179 (tttm) cc_final: 0.6753 (tttp) REVERT: B 304 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7420 (mmt) REVERT: B 325 MET cc_start: 0.9088 (mtp) cc_final: 0.8887 (mtp) REVERT: B 490 MET cc_start: 0.8614 (tmm) cc_final: 0.8361 (tmm) outliers start: 20 outliers final: 6 residues processed: 112 average time/residue: 0.4996 time to fit residues: 59.2462 Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 71 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.118239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.094511 restraints weight = 9716.778| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.39 r_work: 0.2882 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1821 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= 0.130 Angle : 0.603 9.376 11652 Z= 0.302 Chirality : 0.042 0.160 1392 Planarity : 0.005 0.059 1402 Dihedral : 8.412 54.553 1304 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.40 % Allowed : 9.02 % Favored : 88.58 % 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: 1.27 (0.28), residues: 1050 helix: 2.14 (0.20), residues: 748 sheet: -4.07 (0.53), residues: 20 loop : -2.53 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 112 TYR 0.007 0.001 TYR B 500 PHE 0.012 0.001 PHE A 528 TRP 0.020 0.002 TRP A 410 HIS 0.002 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 8532) covalent geometry : angle 0.60288 / 0.30 (11652) hydrogen bonds : bond 0.04909 / 3.28 ( 501) hydrogen bonds : angle 3.60824 / 2.50 ( 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 118 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.221 Fit side-chains REVERT: A 70 MET cc_start: 0.8753 (mtm) cc_final: 0.8395 (mtp) REVERT: A 163 GLN cc_start: 0.7523 (mt0) cc_final: 0.7232 (mt0) REVERT: A 303 LYS cc_start: 0.6974 (tttm) cc_final: 0.6636 (tttp) REVERT: A 318 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7992 (tp30) REVERT: A 490 MET cc_start: 0.8597 (tmm) cc_final: 0.8376 (tmm) REVERT: B 52 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7818 (tp30) REVERT: B 70 MET cc_start: 0.8758 (mtm) cc_final: 0.8405 (mtp) REVERT: B 163 GLN cc_start: 0.7518 (mt0) cc_final: 0.7233 (mt0) REVERT: B 295 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7757 (mtp180) REVERT: B 303 LYS cc_start: 0.6962 (tttm) cc_final: 0.6630 (tttp) REVERT: B 490 MET cc_start: 0.8610 (tmm) cc_final: 0.8394 (tmm) outliers start: 21 outliers final: 8 residues processed: 111 average time/residue: 0.5134 time to fit residues: 60.3676 Evaluate side-chains 105 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 240 THR Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 517 VAL 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: 0.6980 chunk 67 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 59 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- 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 = 0.3331 r_free = 0.3331 target = 0.117655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.093991 restraints weight = 9666.077| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.38 r_work: 0.2876 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1860 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= 0.133 Angle : 0.607 8.281 11652 Z= 0.306 Chirality : 0.043 0.242 1392 Planarity : 0.005 0.060 1402 Dihedral : 8.533 54.412 1304 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.74 % Allowed : 9.13 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.28), residues: 1050 helix: 2.24 (0.20), residues: 748 sheet: -4.01 (0.55), residues: 20 loop : -2.41 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 320 TYR 0.007 0.001 TYR B 500 PHE 0.014 0.001 PHE A 568 TRP 0.021 0.002 TRP B 410 HIS 0.002 0.001 HIS B 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8532) covalent geometry : angle 0.60714 / 0.31 (11652) hydrogen bonds : bond 0.05069 / 3.38 ( 501) hydrogen bonds : angle 3.58970 / 2.50 ( 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 122 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.306 Fit side-chains REVERT: A 163 GLN cc_start: 0.7519 (mt0) cc_final: 0.7200 (mt0) REVERT: A 256 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7033 (pm20) REVERT: A 295 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7577 (mtp180) REVERT: A 303 LYS cc_start: 0.6969 (tttm) cc_final: 0.6589 (tttp) REVERT: A 304 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7431 (mmt) REVERT: A 318 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7900 (tp30) REVERT: A 490 MET cc_start: 0.8575 (tmm) cc_final: 0.8349 (tmm) REVERT: B 52 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7878 (tp30) REVERT: B 163 GLN cc_start: 0.7514 (mt0) cc_final: 0.7197 (mt0) REVERT: B 256 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.7036 (pm20) REVERT: B 303 LYS cc_start: 0.6950 (tttm) cc_final: 0.6575 (tttp) REVERT: B 304 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7446 (mmt) REVERT: B 490 MET cc_start: 0.8569 (tmm) cc_final: 0.8354 (tmm) outliers start: 24 outliers final: 12 residues processed: 113 average time/residue: 0.5257 time to fit residues: 62.8328 Evaluate side-chains 115 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 240 THR Chi-restraints excluded: chain A residue 256 GLN 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 240 THR Chi-restraints excluded: chain B residue 256 GLN 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: 3.9990 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3293 r_free = 0.3293 target = 0.114664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.090972 restraints weight = 9561.311| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.34 r_work: 0.2817 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8532 Z= 0.186 Angle : 0.692 9.314 11652 Z= 0.348 Chirality : 0.047 0.218 1392 Planarity : 0.006 0.060 1402 Dihedral : 9.280 56.229 1304 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.38 % Favored : 95.43 % Rotamer: Outliers : 2.63 % Allowed : 9.36 % Favored : 88.01 % 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: 1.26 (0.27), residues: 1050 helix: 1.95 (0.19), residues: 756 sheet: -3.80 (0.60), residues: 20 loop : -2.11 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 346 TYR 0.011 0.002 TYR B 500 PHE 0.020 0.002 PHE A 568 TRP 0.024 0.002 TRP B 410 HIS 0.004 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 ( 8532) covalent geometry : angle 0.69197 / 0.35 (11652) hydrogen bonds : bond 0.06692 / 4.45 ( 501) hydrogen bonds : angle 3.78397 / 2.64 ( 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 119 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.331 Fit side-chains REVERT: A 18 PHE cc_start: 0.8380 (t80) cc_final: 0.7741 (m-80) REVERT: A 70 MET cc_start: 0.8836 (mtm) cc_final: 0.8509 (mtp) REVERT: A 163 GLN cc_start: 0.7646 (mt0) cc_final: 0.7266 (mt0) REVERT: A 295 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7689 (mtp180) REVERT: A 303 LYS cc_start: 0.6954 (tttm) cc_final: 0.6558 (tttp) REVERT: A 318 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7850 (tp30) REVERT: B 18 PHE cc_start: 0.8366 (t80) cc_final: 0.7738 (m-80) REVERT: B 70 MET cc_start: 0.8840 (mtm) cc_final: 0.8514 (mtp) REVERT: B 163 GLN cc_start: 0.7653 (mt0) cc_final: 0.7280 (mt0) REVERT: B 295 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7743 (mtp180) REVERT: B 303 LYS cc_start: 0.6946 (tttm) cc_final: 0.6558 (tttp) REVERT: B 393 GLN cc_start: 0.7163 (mm-40) cc_final: 0.6941 (mm-40) outliers start: 23 outliers final: 13 residues processed: 109 average time/residue: 0.4970 time to fit residues: 57.4338 Evaluate side-chains 110 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 240 THR 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 240 THR 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: 1.9990 chunk 77 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3290 r_free = 0.3290 target = 0.114565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.090428 restraints weight = 9693.366| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.42 r_work: 0.2825 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8532 Z= 0.174 Angle : 0.674 9.017 11652 Z= 0.341 Chirality : 0.046 0.217 1392 Planarity : 0.006 0.060 1402 Dihedral : 9.658 58.124 1304 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.90 % Favored : 95.90 % Rotamer: Outliers : 2.40 % Allowed : 9.36 % 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: 1.24 (0.27), residues: 1050 helix: 1.85 (0.19), residues: 768 sheet: -3.65 (0.65), residues: 20 loop : -2.01 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 346 TYR 0.009 0.002 TYR B 500 PHE 0.020 0.002 PHE B 568 TRP 0.025 0.002 TRP B 410 HIS 0.003 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 8532) covalent geometry : angle 0.67405 / 0.34 (11652) hydrogen bonds : bond 0.06345 / 4.22 ( 501) hydrogen bonds : angle 3.77097 / 2.62 ( 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 118 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.305 Fit side-chains REVERT: A 18 PHE cc_start: 0.8295 (t80) cc_final: 0.7685 (m-80) REVERT: A 70 MET cc_start: 0.8821 (mtm) cc_final: 0.8482 (mtp) REVERT: A 163 GLN cc_start: 0.7601 (mt0) cc_final: 0.7210 (mt0) REVERT: A 295 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7723 (mtp180) REVERT: A 303 LYS cc_start: 0.6882 (tttm) cc_final: 0.6468 (tttp) REVERT: B 18 PHE cc_start: 0.8274 (t80) cc_final: 0.7673 (m-80) REVERT: B 70 MET cc_start: 0.8828 (mtm) cc_final: 0.8489 (mtp) REVERT: B 85 ASP cc_start: 0.8212 (t70) cc_final: 0.7983 (t70) REVERT: B 163 GLN cc_start: 0.7613 (mt0) cc_final: 0.7228 (mt0) REVERT: B 295 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7726 (mtp180) REVERT: B 303 LYS cc_start: 0.6881 (tttm) cc_final: 0.6473 (tttp) REVERT: B 437 ARG cc_start: 0.8275 (mmt90) cc_final: 0.8048 (mmt90) outliers start: 21 outliers final: 13 residues processed: 108 average time/residue: 0.4954 time to fit residues: 56.7884 Evaluate side-chains 111 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 240 THR 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 240 THR 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: 0.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 102 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3336 r_free = 0.3336 target = 0.118051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.094519 restraints weight = 9640.987| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.37 r_work: 0.2895 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1961 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= 0.127 Angle : 0.595 7.983 11652 Z= 0.303 Chirality : 0.043 0.219 1392 Planarity : 0.005 0.058 1402 Dihedral : 9.236 56.399 1304 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.05 % Allowed : 9.93 % Favored : 88.01 % 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: 1.58 (0.28), residues: 1050 helix: 2.18 (0.19), residues: 772 sheet: -3.59 (0.69), residues: 20 loop : -2.23 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 320 TYR 0.007 0.001 TYR A 40 PHE 0.011 0.001 PHE A 568 TRP 0.023 0.002 TRP A 410 HIS 0.002 0.001 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 8532) covalent geometry : angle 0.59532 / 0.30 (11652) hydrogen bonds : bond 0.04775 / 3.19 ( 501) hydrogen bonds : angle 3.62968 / 2.52 ( 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 113 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.206 Fit side-chains REVERT: A 18 PHE cc_start: 0.8278 (t80) cc_final: 0.7689 (m-80) REVERT: A 70 MET cc_start: 0.8756 (mtm) cc_final: 0.8488 (mtp) REVERT: A 163 GLN cc_start: 0.7492 (mt0) cc_final: 0.7194 (mt0) REVERT: A 256 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.6951 (pm20) REVERT: A 303 LYS cc_start: 0.6870 (tttm) cc_final: 0.6459 (tttp) REVERT: A 437 ARG cc_start: 0.8238 (mmt90) cc_final: 0.8025 (mmt90) REVERT: B 18 PHE cc_start: 0.8246 (t80) cc_final: 0.7683 (m-80) REVERT: B 52 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7903 (tp30) REVERT: B 70 MET cc_start: 0.8762 (mtm) cc_final: 0.8492 (mtp) REVERT: B 163 GLN cc_start: 0.7511 (mt0) cc_final: 0.7179 (mt0) REVERT: B 256 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6948 (pm20) REVERT: B 303 LYS cc_start: 0.6871 (tttm) cc_final: 0.6468 (tttp) REVERT: B 437 ARG cc_start: 0.8182 (mmt90) cc_final: 0.7946 (mmt90) outliers start: 18 outliers final: 11 residues processed: 107 average time/residue: 0.5018 time to fit residues: 56.8902 Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 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 240 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 256 GLN 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: 4.9990 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 0.0470 chunk 52 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.119286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.095839 restraints weight = 9724.497| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.39 r_work: 0.2900 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8532 Z= 0.123 Angle : 0.583 7.838 11652 Z= 0.296 Chirality : 0.042 0.230 1392 Planarity : 0.005 0.058 1402 Dihedral : 8.946 55.260 1304 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.83 % Allowed : 11.19 % Favored : 86.99 % 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: 1.71 (0.28), residues: 1050 helix: 2.42 (0.19), residues: 756 sheet: -3.46 (0.71), residues: 20 loop : -2.40 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 320 TYR 0.007 0.001 TYR B 40 PHE 0.010 0.001 PHE A 351 TRP 0.022 0.002 TRP B 410 HIS 0.003 0.001 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 8532) covalent geometry : angle 0.58328 / 0.30 (11652) hydrogen bonds : bond 0.04419 / 2.95 ( 501) hydrogen bonds : angle 3.53894 / 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: 16 poor density : 97 time to evaluate : 0.279 Fit side-chains REVERT: A 18 PHE cc_start: 0.8227 (t80) cc_final: 0.7662 (m-80) REVERT: A 73 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8462 (m) REVERT: A 163 GLN cc_start: 0.7480 (mt0) cc_final: 0.7247 (mt0) REVERT: A 256 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6875 (pm20) REVERT: A 303 LYS cc_start: 0.6832 (tttm) cc_final: 0.6428 (tttp) REVERT: B 18 PHE cc_start: 0.8197 (t80) cc_final: 0.7605 (m-80) REVERT: B 52 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7885 (tp30) REVERT: B 163 GLN cc_start: 0.7484 (mt0) cc_final: 0.7253 (mt0) REVERT: B 256 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6876 (pm20) REVERT: B 295 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7619 (mtp180) REVERT: B 303 LYS cc_start: 0.6834 (tttm) cc_final: 0.6437 (tttp) outliers start: 16 outliers final: 10 residues processed: 108 average time/residue: 0.4998 time to fit residues: 57.2571 Evaluate side-chains 110 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 240 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 256 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 86 optimal weight: 0.0670 chunk 35 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN B 286 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.096917 restraints weight = 9649.932| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.37 r_work: 0.2933 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2168 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= 0.119 Angle : 0.574 7.580 11652 Z= 0.291 Chirality : 0.042 0.238 1392 Planarity : 0.005 0.058 1402 Dihedral : 8.761 54.868 1304 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.94 % Allowed : 11.42 % Favored : 86.64 % 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: 1.86 (0.28), residues: 1050 helix: 2.55 (0.19), residues: 744 sheet: -3.47 (0.72), residues: 20 loop : -2.21 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 320 TYR 0.007 0.001 TYR B 40 PHE 0.010 0.001 PHE A 351 TRP 0.022 0.001 TRP B 410 HIS 0.004 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 8532) covalent geometry : angle 0.57401 / 0.29 (11652) hydrogen bonds : bond 0.04161 / 2.78 ( 501) hydrogen bonds : angle 3.50192 / 2.43 ( 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 120 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.309 Fit side-chains REVERT: A 18 PHE cc_start: 0.8188 (t80) cc_final: 0.7610 (m-80) REVERT: A 256 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6843 (pm20) REVERT: A 303 LYS cc_start: 0.6827 (tttm) cc_final: 0.6422 (tttp) REVERT: A 437 ARG cc_start: 0.8086 (mmt90) cc_final: 0.7880 (mmt90) REVERT: B 18 PHE cc_start: 0.8176 (t80) cc_final: 0.7588 (m-80) REVERT: B 52 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7884 (tp30) REVERT: B 163 GLN cc_start: 0.7375 (mt0) cc_final: 0.7148 (mt0) REVERT: B 256 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6841 (pm20) REVERT: B 295 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7621 (mtp180) REVERT: B 303 LYS cc_start: 0.6824 (tttm) cc_final: 0.6424 (tttp) outliers start: 17 outliers final: 12 residues processed: 113 average time/residue: 0.4802 time to fit residues: 57.6603 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 : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 256 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 446 ASN B 393 GLN B 446 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.116641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.092531 restraints weight = 9624.667| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.41 r_work: 0.2858 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2010 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= 0.150 Angle : 0.632 8.357 11652 Z= 0.320 Chirality : 0.044 0.218 1392 Planarity : 0.006 0.061 1402 Dihedral : 9.180 56.926 1304 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.94 % Allowed : 10.96 % 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: 1.65 (0.28), residues: 1050 helix: 2.30 (0.19), residues: 756 sheet: -3.44 (0.73), residues: 20 loop : -2.15 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 346 TYR 0.009 0.001 TYR B 500 PHE 0.015 0.002 PHE A 528 TRP 0.022 0.002 TRP A 410 HIS 0.005 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 8532) covalent geometry : angle 0.63191 / 0.32 (11652) hydrogen bonds : bond 0.05530 / 3.68 ( 501) hydrogen bonds : angle 3.61059 / 2.51 ( 1491) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2541.17 seconds wall clock time: 43 minutes 48.57 seconds (2628.57 seconds total)