Starting phenix.real_space_refine on Thu Mar 5 23:32:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i66_52651/03_2026/9i66_52651_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i66_52651/03_2026/9i66_52651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i66_52651/03_2026/9i66_52651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i66_52651/03_2026/9i66_52651.map" model { file = "/net/cci-nas-00/data/ceres_data/9i66_52651/03_2026/9i66_52651_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i66_52651/03_2026/9i66_52651_trim.cif" } resolution = 3.57 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= -0.005 sd= 0.118 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 9 5.49 5 S 48 5.16 5 C 8262 2.51 5 N 1977 2.21 5 O 2190 1.98 5 H 12129 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24615 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 8054 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 13, 'TRANS': 513} Chain: "B" Number of atoms: 8054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 8054 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 13, 'TRANS': 513} Chain: "C" Number of atoms: 8054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 8054 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 13, 'TRANS': 513} Chain: "A" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 302 Unusual residues: {'CDL': 2, 'PGT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.44, per 1000 atoms: 0.18 Number of scatterers: 24615 At special positions: 0 Unit cell: (111.668, 116.985, 77.6355, 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 48 16.00 P 9 15.00 O 2190 8.00 N 1977 7.00 C 8262 6.00 H 12129 1.00 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: 2.22 Conformation dependent library (CDL) restraints added in 798.3 milliseconds 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2826 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 0 sheets defined 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 59 through 80 Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 80 through 120 removed outlier: 3.838A pdb=" N ASP A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N TRP A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ALA A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 removed outlier: 3.876A pdb=" N THR A 124 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 148 removed outlier: 4.186A pdb=" N PHE A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 168 Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 177 through 190 Processing helix chain 'A' and resid 191 through 210 Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 221 through 232 removed outlier: 7.086A pdb=" N GLU A 227 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N LYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 268 Processing helix chain 'A' and resid 277 through 296 Processing helix chain 'A' and resid 299 through 323 removed outlier: 3.571A pdb=" N GLN A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 350 Proline residue: A 334 - end of helix removed outlier: 5.572A pdb=" N PHE A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLN A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 368 through 377 Processing helix chain 'A' and resid 377 through 389 removed outlier: 3.596A pdb=" N VAL A 381 " --> pdb=" O TRP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 427 Proline residue: A 405 - end of helix removed outlier: 3.869A pdb=" N THR A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.712A pdb=" N LEU A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 Processing helix chain 'A' and resid 488 through 509 Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 513 through 527 removed outlier: 3.717A pdb=" N ASN A 517 " --> pdb=" O ASN A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 546 removed outlier: 3.902A pdb=" N VAL A 532 " --> pdb=" O PRO A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 579 Processing helix chain 'B' and resid 59 through 80 Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 80 through 120 removed outlier: 3.884A pdb=" N ASP B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TRP B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ALA B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 112 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 125 removed outlier: 3.827A pdb=" N THR B 124 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 150 removed outlier: 3.988A pdb=" N SER B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET B 150 " --> pdb=" O PHE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 168 Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 177 through 190 Processing helix chain 'B' and resid 191 through 210 Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 221 through 233 removed outlier: 3.579A pdb=" N ILE B 225 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLU B 227 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.611A pdb=" N LYS B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP B 233 " --> pdb=" O GLY B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 268 Processing helix chain 'B' and resid 277 through 296 removed outlier: 3.718A pdb=" N SER B 296 " --> pdb=" O PHE B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 323 removed outlier: 4.110A pdb=" N ILE B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 349 removed outlier: 3.683A pdb=" N LEU B 330 " --> pdb=" O THR B 326 " (cutoff:3.500A) Proline residue: B 334 - end of helix removed outlier: 5.774A pdb=" N PHE B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLN B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 368 through 389 Proline residue: B 379 - end of helix Processing helix chain 'B' and resid 393 through 426 Proline residue: B 405 - end of helix removed outlier: 3.786A pdb=" N THR B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 413 " --> pdb=" O SER B 409 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA B 420 " --> pdb=" O PHE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 446 Processing helix chain 'B' and resid 449 through 481 removed outlier: 5.372A pdb=" N MET B 476 " --> pdb=" O ALA B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 509 Processing helix chain 'B' and resid 510 through 512 No H-bonds generated for 'chain 'B' and resid 510 through 512' Processing helix chain 'B' and resid 513 through 527 Processing helix chain 'B' and resid 528 through 546 removed outlier: 4.105A pdb=" N VAL B 532 " --> pdb=" O PRO B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 549 No H-bonds generated for 'chain 'B' and resid 547 through 549' Processing helix chain 'B' and resid 550 through 579 Processing helix chain 'C' and resid 59 through 80 Proline residue: C 65 - end of helix Processing helix chain 'C' and resid 80 through 119 removed outlier: 3.786A pdb=" N ASP C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TRP C 101 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ALA C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE C 112 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 removed outlier: 3.747A pdb=" N THR C 124 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 147 removed outlier: 4.112A pdb=" N ALA C 147 " --> pdb=" O SER C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 removed outlier: 4.453A pdb=" N THR C 159 " --> pdb=" O MET C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 168 Processing helix chain 'C' and resid 177 through 190 Processing helix chain 'C' and resid 190 through 210 removed outlier: 4.178A pdb=" N TRP C 194 " --> pdb=" O THR C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 221 Processing helix chain 'C' and resid 221 through 232 removed outlier: 3.547A pdb=" N ILE C 225 " --> pdb=" O PHE C 221 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLU C 227 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N LYS C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 268 Processing helix chain 'C' and resid 277 through 296 Processing helix chain 'C' and resid 299 through 323 Processing helix chain 'C' and resid 326 through 350 Proline residue: C 334 - end of helix removed outlier: 5.636A pdb=" N PHE C 345 " --> pdb=" O LEU C 341 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLN C 346 " --> pdb=" O SER C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 357 removed outlier: 4.183A pdb=" N ASP C 356 " --> pdb=" O MET C 353 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY C 357 " --> pdb=" O SER C 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 353 through 357' Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 367 through 389 removed outlier: 3.669A pdb=" N TRP C 371 " --> pdb=" O THR C 367 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE C 375 " --> pdb=" O TRP C 371 " (cutoff:3.500A) Proline residue: C 379 - end of helix Processing helix chain 'C' and resid 393 through 427 Proline residue: C 405 - end of helix removed outlier: 3.927A pdb=" N THR C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 446 Processing helix chain 'C' and resid 449 through 481 Processing helix chain 'C' and resid 488 through 509 Processing helix chain 'C' and resid 510 through 512 No H-bonds generated for 'chain 'C' and resid 510 through 512' Processing helix chain 'C' and resid 513 through 527 Processing helix chain 'C' and resid 528 through 546 removed outlier: 3.920A pdb=" N VAL C 532 " --> pdb=" O PRO C 528 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 580 976 hydrogen bonds defined for protein. 2916 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: 5.23 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12126 1.03 - 1.23: 22 1.23 - 1.42: 5321 1.42 - 1.61: 7347 1.61 - 1.81: 99 Bond restraints: 24915 Sorted by residual: bond pdb=" N THR B 54 " pdb=" CA THR B 54 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.43e+00 bond pdb=" N THR A 54 " pdb=" CA THR A 54 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N THR C 54 " pdb=" CA THR C 54 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N THR C 54 " pdb=" H THR C 54 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" N THR A 54 " pdb=" H THR A 54 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.21e+00 ... (remaining 24910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 43184 1.66 - 3.31: 1327 3.31 - 4.97: 102 4.97 - 6.63: 27 6.63 - 8.28: 9 Bond angle restraints: 44649 Sorted by residual: angle pdb=" N ILE C 270 " pdb=" CA ILE C 270 " pdb=" C ILE C 270 " ideal model delta sigma weight residual 111.90 108.54 3.36 8.10e-01 1.52e+00 1.72e+01 angle pdb=" CA TRP A 377 " pdb=" CB TRP A 377 " pdb=" CG TRP A 377 " ideal model delta sigma weight residual 113.60 119.21 -5.61 1.90e+00 2.77e-01 8.73e+00 angle pdb=" CA TRP B 377 " pdb=" CB TRP B 377 " pdb=" CG TRP B 377 " ideal model delta sigma weight residual 113.60 118.73 -5.13 1.90e+00 2.77e-01 7.28e+00 angle pdb=" CA6 CDL C 601 " pdb=" CA4 CDL C 601 " pdb=" OA6 CDL C 601 " ideal model delta sigma weight residual 107.81 101.45 6.36 2.43e+00 1.69e-01 6.86e+00 angle pdb=" CB2 CDL C 601 " pdb=" C1 CDL C 601 " pdb=" CA2 CDL C 601 " ideal model delta sigma weight residual 113.28 105.38 7.90 3.06e+00 1.07e-01 6.64e+00 ... (remaining 44644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.69: 10254 18.69 - 37.37: 1090 37.37 - 56.06: 410 56.06 - 74.75: 102 74.75 - 93.44: 33 Dihedral angle restraints: 11889 sinusoidal: 6399 harmonic: 5490 Sorted by residual: dihedral pdb=" CA ALA B 472 " pdb=" C ALA B 472 " pdb=" N SER B 473 " pdb=" CA SER B 473 " ideal model delta harmonic sigma weight residual 180.00 152.23 27.77 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA TRP A 377 " pdb=" C TRP A 377 " pdb=" N SER A 378 " pdb=" CA SER A 378 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA GLY A 149 " pdb=" C GLY A 149 " pdb=" N MET A 150 " pdb=" CA MET A 150 " ideal model delta harmonic sigma weight residual -180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 11886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1751 0.067 - 0.134: 194 0.134 - 0.201: 11 0.201 - 0.268: 0 0.268 - 0.336: 6 Chirality restraints: 1962 Sorted by residual: chirality pdb=" CB4 CDL C 601 " pdb=" CB3 CDL C 601 " pdb=" CB6 CDL C 601 " pdb=" OB6 CDL C 601 " both_signs ideal model delta sigma weight residual False -2.57 -2.91 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA4 CDL C 601 " pdb=" CA3 CDL C 601 " pdb=" CA6 CDL C 601 " pdb=" OA6 CDL C 601 " both_signs ideal model delta sigma weight residual False -2.57 -2.91 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA4 CDL A 603 " pdb=" CA3 CDL A 603 " pdb=" CA6 CDL A 603 " pdb=" OA6 CDL A 603 " both_signs ideal model delta sigma weight residual False -2.57 -2.91 0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 1959 not shown) Planarity restraints: 3639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 472 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.07e+00 pdb=" C ALA B 472 " -0.049 2.00e-02 2.50e+03 pdb=" O ALA B 472 " 0.018 2.00e-02 2.50e+03 pdb=" N SER B 473 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 414 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" C SER C 414 " -0.030 2.00e-02 2.50e+03 pdb=" O SER C 414 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE C 415 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 573 " -0.014 2.00e-02 2.50e+03 1.10e-02 2.71e+00 pdb=" CG HIS B 573 " 0.029 2.00e-02 2.50e+03 pdb=" ND1 HIS B 573 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS B 573 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS B 573 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS B 573 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 HIS B 573 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 HIS B 573 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS B 573 " -0.002 2.00e-02 2.50e+03 ... (remaining 3636 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 2556 2.25 - 2.84: 54221 2.84 - 3.43: 67912 3.43 - 4.01: 88716 4.01 - 4.60: 137079 Nonbonded interactions: 350484 Sorted by model distance: nonbonded pdb=" OE1 GLU C 437 " pdb=" H GLU C 437 " model vdw 1.664 2.450 nonbonded pdb=" O ALA B 359 " pdb=" H LEU B 363 " model vdw 1.714 2.450 nonbonded pdb=" O MET C 186 " pdb=" HG1 THR C 190 " model vdw 1.724 2.450 nonbonded pdb=" O ASP A 131 " pdb="HD22 ASN B 560 " model vdw 1.741 2.450 nonbonded pdb=" O ASN B 98 " pdb=" HE1 TRP B 101 " model vdw 1.746 2.450 ... (remaining 350479 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 54 through 580) selection = (chain 'B' and resid 54 through 580) selection = (chain 'C' and resid 54 through 580) } 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 group one per residue 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: 4.690 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: 0.170 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 22.890 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12786 Z= 0.180 Angle : 0.694 8.283 17313 Z= 0.371 Chirality : 0.044 0.336 1962 Planarity : 0.004 0.040 2100 Dihedral : 16.363 93.437 4551 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.21), residues: 1575 helix: 1.29 (0.14), residues: 1275 sheet: None (None), residues: 0 loop : -1.23 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 213 TYR 0.009 0.001 TYR B 370 PHE 0.020 0.002 PHE A 384 TRP 0.020 0.001 TRP A 377 HIS 0.013 0.001 HIS B 573 Details of bonding type rmsd covalent geometry : bond 0.00399 (12786) covalent geometry : angle 0.69356 (17313) hydrogen bonds : bond 0.06444 ( 976) hydrogen bonds : angle 4.75323 ( 2916) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 MET cc_start: 0.7586 (ttt) cc_final: 0.7367 (mtp) REVERT: B 182 MET cc_start: 0.7735 (mmm) cc_final: 0.7528 (mmm) REVERT: C 459 ILE cc_start: 0.8271 (mm) cc_final: 0.8057 (mp) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.2270 time to fit residues: 63.8374 Evaluate side-chains 119 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.141634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121163 restraints weight = 52899.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.125329 restraints weight = 29617.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.128172 restraints weight = 20183.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.130026 restraints weight = 15321.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.131359 restraints weight = 12566.415| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12786 Z= 0.180 Angle : 0.535 6.578 17313 Z= 0.302 Chirality : 0.037 0.140 1962 Planarity : 0.004 0.037 2100 Dihedral : 13.036 91.326 2088 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.57 % Allowed : 8.68 % Favored : 90.75 % 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 (0.22), residues: 1575 helix: 1.59 (0.14), residues: 1278 sheet: None (None), residues: 0 loop : -1.01 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 210 TYR 0.008 0.001 TYR B 370 PHE 0.014 0.001 PHE B 156 TRP 0.016 0.001 TRP A 377 HIS 0.005 0.001 HIS B 573 Details of bonding type rmsd covalent geometry : bond 0.00392 (12786) covalent geometry : angle 0.53506 (17313) hydrogen bonds : bond 0.04467 ( 976) hydrogen bonds : angle 4.39307 ( 2916) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 459 ILE cc_start: 0.8374 (mm) cc_final: 0.8120 (mp) outliers start: 7 outliers final: 7 residues processed: 134 average time/residue: 0.1892 time to fit residues: 39.6103 Evaluate side-chains 126 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 563 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 103 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 445 HIS C 556 GLN C 557 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.140662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.120016 restraints weight = 53037.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124203 restraints weight = 30017.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.127045 restraints weight = 20497.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128917 restraints weight = 15614.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.130224 restraints weight = 12805.110| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12786 Z= 0.165 Angle : 0.515 6.448 17313 Z= 0.290 Chirality : 0.036 0.159 1962 Planarity : 0.003 0.032 2100 Dihedral : 12.261 89.446 2088 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.81 % Allowed : 10.30 % Favored : 88.89 % 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: 1.81 (0.22), residues: 1575 helix: 1.67 (0.14), residues: 1284 sheet: None (None), residues: 0 loop : -0.82 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.014 0.001 TYR C 553 PHE 0.014 0.001 PHE B 156 TRP 0.013 0.001 TRP A 377 HIS 0.005 0.001 HIS B 573 Details of bonding type rmsd covalent geometry : bond 0.00360 (12786) covalent geometry : angle 0.51479 (17313) hydrogen bonds : bond 0.04329 ( 976) hydrogen bonds : angle 4.28778 ( 2916) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 459 ILE cc_start: 0.8390 (mm) cc_final: 0.8111 (mp) outliers start: 10 outliers final: 6 residues processed: 131 average time/residue: 0.2032 time to fit residues: 41.7360 Evaluate side-chains 124 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 563 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 556 GLN C 557 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.140738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.119912 restraints weight = 53075.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124135 restraints weight = 30079.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.126990 restraints weight = 20577.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.128903 restraints weight = 15711.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.130180 restraints weight = 12885.821| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12786 Z= 0.155 Angle : 0.498 6.331 17313 Z= 0.281 Chirality : 0.036 0.139 1962 Planarity : 0.003 0.032 2100 Dihedral : 11.725 87.561 2088 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.81 % Allowed : 11.52 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.22), residues: 1575 helix: 1.82 (0.15), residues: 1278 sheet: None (None), residues: 0 loop : -0.91 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.015 0.001 TYR C 553 PHE 0.014 0.001 PHE B 156 TRP 0.014 0.001 TRP A 377 HIS 0.006 0.001 HIS B 573 Details of bonding type rmsd covalent geometry : bond 0.00335 (12786) covalent geometry : angle 0.49774 (17313) hydrogen bonds : bond 0.04209 ( 976) hydrogen bonds : angle 4.21497 ( 2916) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 459 ILE cc_start: 0.8312 (mm) cc_final: 0.8072 (mp) outliers start: 10 outliers final: 9 residues processed: 130 average time/residue: 0.2058 time to fit residues: 41.7470 Evaluate side-chains 130 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 563 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 107 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS C 556 GLN C 557 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.138551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.117100 restraints weight = 53290.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.121328 restraints weight = 30471.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124208 restraints weight = 20990.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.126051 restraints weight = 16089.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.127383 restraints weight = 13351.933| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12786 Z= 0.196 Angle : 0.527 6.293 17313 Z= 0.299 Chirality : 0.037 0.141 1962 Planarity : 0.003 0.035 2100 Dihedral : 11.318 86.370 2088 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.54 % Allowed : 12.73 % Favored : 85.73 % 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: 1.90 (0.22), residues: 1575 helix: 1.73 (0.14), residues: 1284 sheet: None (None), residues: 0 loop : -0.78 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.006 0.001 TYR B 553 PHE 0.016 0.002 PHE B 156 TRP 0.016 0.001 TRP A 377 HIS 0.007 0.001 HIS B 573 Details of bonding type rmsd covalent geometry : bond 0.00436 (12786) covalent geometry : angle 0.52746 (17313) hydrogen bonds : bond 0.04411 ( 976) hydrogen bonds : angle 4.28162 ( 2916) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 459 ILE cc_start: 0.8404 (mm) cc_final: 0.8090 (mp) outliers start: 19 outliers final: 15 residues processed: 136 average time/residue: 0.2005 time to fit residues: 42.5771 Evaluate side-chains 136 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 369 PHE Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 563 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.137909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.116568 restraints weight = 53205.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120780 restraints weight = 30336.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.123630 restraints weight = 20862.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.125531 restraints weight = 16029.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.126788 restraints weight = 13230.000| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12786 Z= 0.204 Angle : 0.537 6.295 17313 Z= 0.303 Chirality : 0.037 0.140 1962 Planarity : 0.003 0.037 2100 Dihedral : 11.133 85.448 2088 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.95 % Allowed : 12.98 % Favored : 85.08 % 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: 1.82 (0.22), residues: 1575 helix: 1.67 (0.14), residues: 1284 sheet: None (None), residues: 0 loop : -0.81 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.012 0.001 TYR C 553 PHE 0.015 0.002 PHE B 156 TRP 0.016 0.001 TRP A 377 HIS 0.007 0.001 HIS B 573 Details of bonding type rmsd covalent geometry : bond 0.00455 (12786) covalent geometry : angle 0.53668 (17313) hydrogen bonds : bond 0.04431 ( 976) hydrogen bonds : angle 4.31912 ( 2916) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 459 ILE cc_start: 0.8316 (mm) cc_final: 0.7994 (mp) outliers start: 24 outliers final: 19 residues processed: 137 average time/residue: 0.2005 time to fit residues: 43.2894 Evaluate side-chains 132 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 369 PHE Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 563 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 82 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 121 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.139538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118277 restraints weight = 53107.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.122548 restraints weight = 30038.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.125470 restraints weight = 20579.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.127382 restraints weight = 15694.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.128493 restraints weight = 12902.574| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12786 Z= 0.148 Angle : 0.506 6.925 17313 Z= 0.282 Chirality : 0.036 0.139 1962 Planarity : 0.003 0.036 2100 Dihedral : 10.711 84.181 2088 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.38 % Allowed : 13.79 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.22), residues: 1575 helix: 1.85 (0.15), residues: 1278 sheet: None (None), residues: 0 loop : -0.93 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.007 0.001 TYR C 553 PHE 0.013 0.001 PHE B 146 TRP 0.012 0.001 TRP A 377 HIS 0.007 0.001 HIS B 573 Details of bonding type rmsd covalent geometry : bond 0.00322 (12786) covalent geometry : angle 0.50562 (17313) hydrogen bonds : bond 0.04179 ( 976) hydrogen bonds : angle 4.19470 ( 2916) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 459 ILE cc_start: 0.8305 (mm) cc_final: 0.7984 (mt) outliers start: 17 outliers final: 13 residues processed: 137 average time/residue: 0.1938 time to fit residues: 42.0491 Evaluate side-chains 134 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 369 PHE Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 563 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 5 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.139527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.118249 restraints weight = 53143.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.122550 restraints weight = 30257.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.125449 restraints weight = 20687.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.127374 restraints weight = 15808.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.128675 restraints weight = 12974.563| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12786 Z= 0.150 Angle : 0.503 6.219 17313 Z= 0.281 Chirality : 0.036 0.139 1962 Planarity : 0.003 0.036 2100 Dihedral : 10.428 83.398 2088 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.46 % Allowed : 14.27 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.22), residues: 1575 helix: 1.86 (0.15), residues: 1281 sheet: None (None), residues: 0 loop : -0.84 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.007 0.001 TYR B 553 PHE 0.015 0.001 PHE A 113 TRP 0.013 0.001 TRP A 377 HIS 0.007 0.001 HIS B 573 Details of bonding type rmsd covalent geometry : bond 0.00327 (12786) covalent geometry : angle 0.50273 (17313) hydrogen bonds : bond 0.04141 ( 976) hydrogen bonds : angle 4.16683 ( 2916) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 459 ILE cc_start: 0.8320 (mm) cc_final: 0.7989 (mt) outliers start: 18 outliers final: 17 residues processed: 138 average time/residue: 0.1966 time to fit residues: 42.6857 Evaluate side-chains 140 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 369 PHE Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 563 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 151 optimal weight: 0.9990 chunk 28 optimal weight: 0.0870 chunk 94 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.141134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.120313 restraints weight = 53006.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.124560 restraints weight = 30065.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.127444 restraints weight = 20552.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.129370 restraints weight = 15620.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.130628 restraints weight = 12791.071| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12786 Z= 0.121 Angle : 0.484 6.440 17313 Z= 0.268 Chirality : 0.035 0.140 1962 Planarity : 0.003 0.034 2100 Dihedral : 9.988 82.083 2088 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.30 % Allowed : 14.52 % Favored : 84.18 % 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: 2.22 (0.22), residues: 1575 helix: 2.00 (0.15), residues: 1278 sheet: None (None), residues: 0 loop : -0.89 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.007 0.001 TYR B 370 PHE 0.013 0.001 PHE A 384 TRP 0.010 0.001 TRP A 377 HIS 0.007 0.001 HIS B 573 Details of bonding type rmsd covalent geometry : bond 0.00256 (12786) covalent geometry : angle 0.48443 (17313) hydrogen bonds : bond 0.03906 ( 976) hydrogen bonds : angle 4.06171 ( 2916) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 LYS cc_start: 0.7912 (pttt) cc_final: 0.7189 (mmmt) REVERT: B 495 TRP cc_start: 0.7418 (m100) cc_final: 0.7087 (m100) REVERT: C 459 ILE cc_start: 0.8298 (mm) cc_final: 0.7967 (mt) outliers start: 16 outliers final: 15 residues processed: 142 average time/residue: 0.1894 time to fit residues: 42.3891 Evaluate side-chains 142 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 369 PHE Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 563 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 74 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.137627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116173 restraints weight = 53308.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120311 restraints weight = 30653.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.123183 restraints weight = 21243.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125093 restraints weight = 16337.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.126181 restraints weight = 13489.533| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12786 Z= 0.212 Angle : 0.546 6.177 17313 Z= 0.308 Chirality : 0.037 0.142 1962 Planarity : 0.003 0.037 2100 Dihedral : 10.193 82.800 2088 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.46 % Allowed : 14.68 % Favored : 83.86 % 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 (0.22), residues: 1575 helix: 1.80 (0.15), residues: 1284 sheet: None (None), residues: 0 loop : -0.82 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.007 0.001 TYR B 553 PHE 0.015 0.002 PHE B 156 TRP 0.018 0.001 TRP A 377 HIS 0.007 0.001 HIS B 573 Details of bonding type rmsd covalent geometry : bond 0.00475 (12786) covalent geometry : angle 0.54572 (17313) hydrogen bonds : bond 0.04339 ( 976) hydrogen bonds : angle 4.22556 ( 2916) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 LYS cc_start: 0.7834 (pttt) cc_final: 0.7119 (mmmt) REVERT: B 453 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6760 (mmp) REVERT: C 459 ILE cc_start: 0.8343 (mm) cc_final: 0.7998 (mt) outliers start: 18 outliers final: 15 residues processed: 141 average time/residue: 0.2004 time to fit residues: 44.3525 Evaluate side-chains 141 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 369 PHE Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 377 TRP Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 563 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 87 optimal weight: 0.9990 chunk 45 optimal weight: 0.0870 chunk 25 optimal weight: 0.4980 chunk 16 optimal weight: 0.4980 chunk 73 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 143 optimal weight: 0.0870 chunk 48 optimal weight: 0.9980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.140958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.120200 restraints weight = 52872.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.124480 restraints weight = 29956.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.127326 restraints weight = 20467.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.129224 restraints weight = 15581.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.130228 restraints weight = 12785.332| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12786 Z= 0.113 Angle : 0.485 6.001 17313 Z= 0.268 Chirality : 0.036 0.176 1962 Planarity : 0.003 0.034 2100 Dihedral : 9.755 81.408 2088 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.38 % Allowed : 14.76 % Favored : 83.86 % 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: 2.23 (0.22), residues: 1575 helix: 1.99 (0.15), residues: 1281 sheet: None (None), residues: 0 loop : -0.82 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.011 0.001 TYR C 157 PHE 0.013 0.001 PHE B 441 TRP 0.010 0.001 TRP A 194 HIS 0.007 0.001 HIS B 573 Details of bonding type rmsd covalent geometry : bond 0.00235 (12786) covalent geometry : angle 0.48547 (17313) hydrogen bonds : bond 0.03881 ( 976) hydrogen bonds : angle 4.05827 ( 2916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3179.84 seconds wall clock time: 55 minutes 5.10 seconds (3305.10 seconds total)