Starting phenix.real_space_refine on Thu Jun 12 07:28:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0r_39713/06_2025/8z0r_39713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0r_39713/06_2025/8z0r_39713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z0r_39713/06_2025/8z0r_39713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0r_39713/06_2025/8z0r_39713.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0r_39713/06_2025/8z0r_39713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0r_39713/06_2025/8z0r_39713.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.059 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: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 8702 2.51 5 N 2448 2.21 5 O 2535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13717 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3384 Classifications: {'peptide': 439} Incomplete info: {'backbone_only': 3, 'n_c_alpha_c_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 29, 'TRANS': 409} Unresolved chain links: 1 Unresolved chain link angles: 10 Unresolved chain link dihedrals: 15 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3452 Classifications: {'peptide': 443} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 412} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 6 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3398 Classifications: {'peptide': 438} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 29, 'TRANS': 408} Unresolved chain links: 1 Unresolved chain link angles: 5 Unresolved chain link dihedrals: 7 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 3483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3483 Classifications: {'peptide': 446} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 415} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 8.02, per 1000 atoms: 0.58 Number of scatterers: 13717 At special positions: 0 Unit cell: (95.76, 101.64, 131.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 2535 8.00 N 2448 7.00 C 8702 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: 2.81 Conformation dependent library (CDL) restraints added in 1.8 seconds 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3292 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 12 sheets defined 41.2% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 113 through 117 removed outlier: 3.653A pdb=" N SER A 117 " --> pdb=" O CYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 161 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 244 through 261 Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 333 through 347 Processing helix chain 'A' and resid 350 through 364 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.914A pdb=" N GLU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 426 Processing helix chain 'A' and resid 430 through 438 Processing helix chain 'A' and resid 512 through 521 Processing helix chain 'A' and resid 525 through 533 Processing helix chain 'A' and resid 537 through 546 Processing helix chain 'B' and resid 114 through 119 removed outlier: 3.538A pdb=" N SER B 117 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU B 118 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU B 119 " --> pdb=" O GLN B 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 114 through 119' Processing helix chain 'B' and resid 146 through 161 Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 194 through 206 removed outlier: 3.525A pdb=" N VAL B 198 " --> pdb=" O GLY B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 262 removed outlier: 4.161A pdb=" N ARG B 262 " --> pdb=" O GLN B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 287 through 302 Processing helix chain 'B' and resid 333 through 347 Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.221A pdb=" N GLU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 426 Processing helix chain 'B' and resid 430 through 439 Processing helix chain 'B' and resid 512 through 533 removed outlier: 3.644A pdb=" N LEU B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 546 Processing helix chain 'C' and resid 114 through 119 removed outlier: 4.088A pdb=" N GLU C 118 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C 119 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 161 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 194 through 206 Processing helix chain 'C' and resid 242 through 262 removed outlier: 4.327A pdb=" N ARG C 262 " --> pdb=" O GLN C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 286 Processing helix chain 'C' and resid 288 through 302 Processing helix chain 'C' and resid 333 through 346 Processing helix chain 'C' and resid 350 through 364 Processing helix chain 'C' and resid 365 through 367 No H-bonds generated for 'chain 'C' and resid 365 through 367' Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.704A pdb=" N GLU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG C 388 " --> pdb=" O GLU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 426 Processing helix chain 'C' and resid 430 through 439 Processing helix chain 'C' and resid 512 through 533 removed outlier: 3.685A pdb=" N LEU C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 546 Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.859A pdb=" N GLU D 118 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU D 119 " --> pdb=" O GLN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 242 through 262 removed outlier: 4.101A pdb=" N ARG D 262 " --> pdb=" O GLN D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 285 Processing helix chain 'D' and resid 288 through 302 Processing helix chain 'D' and resid 333 through 348 Processing helix chain 'D' and resid 350 through 364 Processing helix chain 'D' and resid 383 through 389 removed outlier: 3.731A pdb=" N GLU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG D 388 " --> pdb=" O GLU D 385 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 389 " --> pdb=" O LEU D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 426 Processing helix chain 'D' and resid 430 through 439 Processing helix chain 'D' and resid 512 through 533 removed outlier: 3.601A pdb=" N LEU D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 546 Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 191 removed outlier: 6.522A pdb=" N ALA A 188 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR A 224 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU A 190 " --> pdb=" O THR A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 171 Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 332 removed outlier: 3.551A pdb=" N ARG A 494 " --> pdb=" O ARG A 501 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A 495 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 10.547A pdb=" N VAL A 452 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA A 373 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE A 454 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLY A 375 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU A 456 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 109 through 111 Processing sheet with id=AA5, first strand: chain 'B' and resid 188 through 191 removed outlier: 6.561A pdb=" N ALA B 188 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N THR B 224 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU B 190 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N THR B 226 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLU B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 325 through 332 removed outlier: 4.157A pdb=" N GLU B 495 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 10.588A pdb=" N VAL B 452 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ALA B 373 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N PHE B 454 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY B 375 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU B 456 " --> pdb=" O GLY B 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 110 through 111 Processing sheet with id=AA8, first strand: chain 'C' and resid 188 through 191 removed outlier: 6.415A pdb=" N ALA C 188 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N THR C 224 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU C 190 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N THR C 226 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU C 229 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA C 138 " --> pdb=" O LEU C 478 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 325 through 332 removed outlier: 6.569A pdb=" N MET C 453 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL C 493 " --> pdb=" O MET C 453 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN C 455 " --> pdb=" O VAL C 493 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLU C 495 " --> pdb=" O ASN C 455 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL C 457 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N VAL C 452 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA C 373 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE C 454 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY C 375 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LEU C 456 " --> pdb=" O GLY C 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 110 through 111 removed outlier: 3.640A pdb=" N THR D 174 " --> pdb=" O ARG D 171 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 188 through 191 removed outlier: 6.474A pdb=" N ALA D 188 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N THR D 224 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU D 190 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N THR D 226 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLU D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 325 through 332 removed outlier: 6.542A pdb=" N MET D 453 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N VAL D 493 " --> pdb=" O MET D 453 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN D 455 " --> pdb=" O VAL D 493 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLU D 495 " --> pdb=" O ASN D 455 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL D 457 " --> pdb=" O GLU D 495 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL D 452 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU D 456 " --> pdb=" O PRO D 377 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N THR D 379 " --> pdb=" O LEU D 456 " (cutoff:3.500A) 698 hydrogen bonds defined for protein. 2004 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: 3.82 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4652 1.34 - 1.46: 2739 1.46 - 1.58: 6596 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 14043 Sorted by residual: bond pdb=" CE1 PHE B 475 " pdb=" CZ PHE B 475 " ideal model delta sigma weight residual 1.382 1.423 -0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" CD1 PHE B 475 " pdb=" CE1 PHE B 475 " ideal model delta sigma weight residual 1.382 1.422 -0.040 3.00e-02 1.11e+03 1.77e+00 bond pdb=" CB PRO D 207 " pdb=" CG PRO D 207 " ideal model delta sigma weight residual 1.492 1.458 0.034 5.00e-02 4.00e+02 4.63e-01 bond pdb=" C TYR B 523 " pdb=" O TYR B 523 " ideal model delta sigma weight residual 1.237 1.244 -0.008 1.17e-02 7.31e+03 4.18e-01 bond pdb=" CB PRO B 442 " pdb=" CG PRO B 442 " ideal model delta sigma weight residual 1.492 1.524 -0.032 5.00e-02 4.00e+02 4.08e-01 ... (remaining 14038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 18618 1.20 - 2.41: 400 2.41 - 3.61: 106 3.61 - 4.81: 16 4.81 - 6.02: 3 Bond angle restraints: 19143 Sorted by residual: angle pdb=" CD1 PHE B 475 " pdb=" CE1 PHE B 475 " pdb=" CZ PHE B 475 " ideal model delta sigma weight residual 120.00 126.02 -6.02 1.80e+00 3.09e-01 1.12e+01 angle pdb=" C GLU D 118 " pdb=" N LEU D 119 " pdb=" CA LEU D 119 " ideal model delta sigma weight residual 121.54 116.16 5.38 1.91e+00 2.74e-01 7.92e+00 angle pdb=" N GLY C 499 " pdb=" CA GLY C 499 " pdb=" C GLY C 499 " ideal model delta sigma weight residual 111.21 114.08 -2.87 1.04e+00 9.25e-01 7.62e+00 angle pdb=" N GLY B 499 " pdb=" CA GLY B 499 " pdb=" C GLY B 499 " ideal model delta sigma weight residual 111.56 114.32 -2.76 1.01e+00 9.80e-01 7.48e+00 angle pdb=" C GLU B 118 " pdb=" N LEU B 119 " pdb=" CA LEU B 119 " ideal model delta sigma weight residual 121.54 116.76 4.78 1.91e+00 2.74e-01 6.26e+00 ... (remaining 19138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 7629 16.84 - 33.67: 636 33.67 - 50.51: 111 50.51 - 67.35: 25 67.35 - 84.18: 14 Dihedral angle restraints: 8415 sinusoidal: 3303 harmonic: 5112 Sorted by residual: dihedral pdb=" CA LEU A 119 " pdb=" C LEU A 119 " pdb=" N TRP A 120 " pdb=" CA TRP A 120 " ideal model delta harmonic sigma weight residual 180.00 159.33 20.67 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA GLU A 118 " pdb=" C GLU A 118 " pdb=" N LEU A 119 " pdb=" CA LEU A 119 " ideal model delta harmonic sigma weight residual -180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LEU B 119 " pdb=" C LEU B 119 " pdb=" N TRP B 120 " pdb=" CA TRP B 120 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 8412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1396 0.030 - 0.059: 474 0.059 - 0.089: 126 0.089 - 0.119: 129 0.119 - 0.148: 8 Chirality restraints: 2133 Sorted by residual: chirality pdb=" CA PHE C 286 " pdb=" N PHE C 286 " pdb=" C PHE C 286 " pdb=" CB PHE C 286 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA VAL A 103 " pdb=" N VAL A 103 " pdb=" C VAL A 103 " pdb=" CB VAL A 103 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA VAL D 330 " pdb=" N VAL D 330 " pdb=" C VAL D 330 " pdb=" CB VAL D 330 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 2130 not shown) Planarity restraints: 2530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 226 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO C 227 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 227 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 227 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 496 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO A 497 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 497 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 497 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 496 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO B 497 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 497 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 497 " -0.027 5.00e-02 4.00e+02 ... (remaining 2527 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1280 2.75 - 3.29: 12443 3.29 - 3.82: 22676 3.82 - 4.36: 26816 4.36 - 4.90: 45718 Nonbonded interactions: 108933 Sorted by model distance: nonbonded pdb=" OG1 THR A 532 " pdb=" OE1 GLN A 533 " model vdw 2.210 3.040 nonbonded pdb=" OG SER A 167 " pdb=" O ASP A 214 " model vdw 2.297 3.040 nonbonded pdb=" NH1 ARG B 381 " pdb=" O LEU B 386 " model vdw 2.299 3.120 nonbonded pdb=" NE2 GLN B 294 " pdb=" OE1 GLU B 428 " model vdw 2.308 3.120 nonbonded pdb=" NH2 ARG A 381 " pdb=" O LEU A 389 " model vdw 2.313 3.120 ... (remaining 108928 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 101 through 117 or (resid 118 and (name N or name CA or na \ me C or name O )) or resid 119 through 264 or (resid 265 and (name N or name CA \ or name C or name O or name CB )) or resid 266 through 288 or (resid 289 and (na \ me N or name CA or name C or name O )) or resid 290 through 303 or (resid 304 an \ d (name N or name CA or name C or name O or name CB )) or resid 305 through 367 \ or (resid 368 and (name N or name CA or name C or name O or name CB or name CG ) \ ) or resid 369 or (resid 370 through 371 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD )) or resid 372 through 384 or (resid 385 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or resid 386 \ through 432 or (resid 433 and (name N or name CA or name C or name O or name CB \ )) or resid 434 through 460 or (resid 471 and (name C or name O )) or resid 472 \ through 474 or (resid 475 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CE1 or name CE2 or name CZ )) or resid 476 throug \ h 539 or (resid 540 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name NE )) or resid 541 through 542 or (resid 543 and (name N \ or name CA or name C or name O or name CB or name CG )) or (resid 544 through 5 \ 47 and (name N or name CA or name C or name O or name CB )) or (resid 548 and (n \ ame N )))) selection = (chain 'B' and (resid 101 through 109 or (resid 110 and (name N or name CA or na \ me C or name O or name CB )) or resid 111 through 117 or (resid 118 and (name N \ or name CA or name C or name O )) or resid 119 through 242 or (resid 243 and (na \ me N or name C or name O )) or resid 244 through 260 or (resid 261 and (name N o \ r name CA or name C or name O )) or resid 262 through 267 or (resid 268 and (nam \ e N or name CA or name C or name O )) or resid 269 through 283 or (resid 284 and \ (name N or name CA or name C or name O or name CB )) or resid 285 through 290 o \ r (resid 291 through 293 and (name N or name CA or name C or name O or name CB ) \ ) or resid 294 through 303 or (resid 304 and (name N or name CA or name C or nam \ e O or name CB )) or resid 305 through 346 or (resid 347 and (name N or name CA \ or name C or name O or name CB )) or resid 348 through 367 or (resid 368 and (na \ me N or name CA or name C or name O or name CB or name CG )) or resid 369 or (re \ sid 370 through 371 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD )) or resid 372 through 382 or (resid 383 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name NE )) or resid 384 \ through 424 or (resid 425 and (name N or name CA or name C or name O or name CB \ or name CG )) or resid 426 through 432 or (resid 433 and (name N or name CA or \ name C or name O or name CB )) or resid 434 through 459 or (resid 460 and (name \ N )) or (resid 471 and (name C or name O )) or resid 472 through 493 or (resid 4 \ 94 and (name N or name CA or name C or name O or name CB )) or resid 495 through \ 500 or (resid 501 and (name N or name CA or name C or name O or name CB )) or r \ esid 502 through 521 or (resid 522 and (name N or name C or name O or name CB or \ name OG1 or name CG2)) or resid 523 through 539 or (resid 540 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD or name NE )) or resi \ d 541 through 542 or (resid 543 and (name N or name CA or name C or name O or na \ me CB or name CG )) or (resid 544 through 547 and (name N or name CA or name C o \ r name O or name CB )) or (resid 548 and (name N )))) selection = (chain 'C' and (resid 101 through 109 or (resid 110 and (name N or name CA or na \ me C or name O or name CB )) or resid 111 through 242 or (resid 243 and (name N \ or name C or name O )) or resid 244 through 260 or (resid 261 and (name N or nam \ e CA or name C or name O )) or resid 262 through 264 or (resid 265 and (name N o \ r name CA or name C or name O or name CB )) or resid 266 through 267 or (resid 2 \ 68 and (name N or name CA or name C or name O )) or resid 269 through 283 or (re \ sid 284 and (name N or name CA or name C or name O or name CB )) or resid 285 th \ rough 290 or (resid 291 through 293 and (name N or name CA or name C or name O o \ r name CB )) or resid 294 through 346 or (resid 347 and (name N or name CA or na \ me C or name O or name CB )) or resid 348 through 382 or (resid 383 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name NE )) or \ resid 384 or (resid 385 and (name N or name CA or name C or name O or name CB o \ r name CG )) or resid 386 through 424 or (resid 425 and (name N or name CA or na \ me C or name O or name CB or name CG )) or resid 426 through 459 or (resid 460 a \ nd (name N )) or resid 471 through 474 or (resid 475 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CE1 or name CE2 or nam \ e CZ )) or resid 476 through 493 or (resid 494 and (name N or name CA or name C \ or name O or name CB )) or resid 495 through 500 or (resid 501 and (name N or na \ me CA or name C or name O or name CB )) or resid 502 through 521 or (resid 522 a \ nd (name N or name C or name O or name CB or name OG1 or name CG2)) or resid 523 \ through 548)) selection = (chain 'D' and (resid 101 through 109 or (resid 110 and (name N or name CA or na \ me C or name O or name CB )) or resid 111 through 117 or (resid 118 and (name N \ or name CA or name C or name O )) or resid 119 through 242 or (resid 243 and (na \ me N or name C or name O )) or resid 244 through 260 or (resid 261 and (name N o \ r name CA or name C or name O )) or resid 262 through 264 or (resid 265 and (nam \ e N or name CA or name C or name O or name CB )) or resid 266 through 267 or (re \ sid 268 and (name N or name CA or name C or name O )) or resid 269 through 283 o \ r (resid 284 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 85 through 290 or (resid 291 through 293 and (name N or name CA or name C or nam \ e O or name CB )) or resid 294 through 303 or (resid 304 and (name N or name CA \ or name C or name O or name CB )) or resid 305 through 346 or (resid 347 and (na \ me N or name CA or name C or name O or name CB )) or resid 348 through 367 or (r \ esid 368 and (name N or name CA or name C or name O or name CB or name CG )) or \ resid 369 or (resid 370 through 371 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD )) or resid 372 through 382 or (resid 383 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name NE \ )) or resid 384 or (resid 385 and (name N or name CA or name C or name O or nam \ e CB or name CG )) or resid 386 through 424 or (resid 425 and (name N or name CA \ or name C or name O or name CB or name CG )) or resid 426 through 432 or (resid \ 433 and (name N or name CA or name C or name O or name CB )) or resid 434 throu \ gh 459 or (resid 460 and (name N )) or (resid 471 and (name C or name O )) or re \ sid 472 through 474 or (resid 475 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CE1 or name CE2 or name CZ )) or resid 47 \ 6 through 493 or (resid 494 and (name N or name CA or name C or name O or name C \ B )) or resid 495 through 500 or (resid 501 and (name N or name CA or name C or \ name O or name CB )) or resid 502 through 521 or (resid 522 and (name N or name \ C or name O or name CB or name OG1 or name CG2)) or resid 523 through 539 or (re \ sid 540 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE )) or resid 541 through 542 or (resid 543 and (name N or name CA \ or name C or name O or name CB or name CG )) or (resid 544 through 547 and (name \ N or name CA or name C or name O or name CB )) or (resid 548 and (name N )))) } 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: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.700 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.050 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:10.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 : 0.002 0.041 14043 Z= 0.097 Angle : 0.468 6.017 19143 Z= 0.251 Chirality : 0.039 0.148 2133 Planarity : 0.005 0.051 2530 Dihedral : 13.215 84.182 5123 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 1741 helix: 1.84 (0.21), residues: 668 sheet: 0.40 (0.25), residues: 416 loop : -0.88 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 120 HIS 0.004 0.001 HIS C 127 PHE 0.015 0.001 PHE A 249 TYR 0.023 0.001 TYR C 150 ARG 0.002 0.000 ARG D 404 Details of bonding type rmsd hydrogen bonds : bond 0.15193 ( 698) hydrogen bonds : angle 5.71271 ( 2004) covalent geometry : bond 0.00210 (14043) covalent geometry : angle 0.46819 (19143) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.573 Fit side-chains REVERT: A 412 LEU cc_start: 0.6093 (tt) cc_final: 0.5703 (tm) REVERT: B 152 ARG cc_start: 0.7827 (mtm180) cc_final: 0.7512 (mtp180) REVERT: B 178 LYS cc_start: 0.8074 (tptm) cc_final: 0.7869 (tptt) REVERT: C 182 THR cc_start: 0.7735 (t) cc_final: 0.7357 (m) REVERT: D 283 ARG cc_start: 0.7972 (ttp-170) cc_final: 0.7536 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 1.8797 time to fit residues: 368.7037 Evaluate side-chains 158 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 0.0570 chunk 70 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN B 148 GLN C 124 GLN C 294 GLN C 417 GLN D 254 ASN D 417 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.186132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.126535 restraints weight = 12968.406| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.11 r_work: 0.3208 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14043 Z= 0.183 Angle : 0.604 6.157 19143 Z= 0.320 Chirality : 0.044 0.157 2133 Planarity : 0.006 0.056 2530 Dihedral : 4.482 19.610 1970 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.25 % Favored : 95.63 % Rotamer: Outliers : 1.20 % Allowed : 7.07 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.20), residues: 1741 helix: 1.85 (0.21), residues: 683 sheet: 0.31 (0.25), residues: 418 loop : -0.94 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 120 HIS 0.005 0.001 HIS C 127 PHE 0.024 0.003 PHE C 241 TYR 0.032 0.002 TYR C 150 ARG 0.006 0.001 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.05765 ( 698) hydrogen bonds : angle 4.72690 ( 2004) covalent geometry : bond 0.00432 (14043) covalent geometry : angle 0.60370 (19143) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 1.407 Fit side-chains REVERT: A 428 GLU cc_start: 0.5581 (tp30) cc_final: 0.3995 (tt0) REVERT: B 178 LYS cc_start: 0.8092 (tptm) cc_final: 0.7568 (tptt) REVERT: B 252 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: B 417 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: C 170 ARG cc_start: 0.7991 (ttt-90) cc_final: 0.7778 (ttt90) REVERT: C 182 THR cc_start: 0.7630 (t) cc_final: 0.7117 (m) REVERT: C 299 ARG cc_start: 0.7922 (ttp-110) cc_final: 0.7614 (ttp-110) REVERT: C 385 GLU cc_start: 0.7097 (mp0) cc_final: 0.6805 (mp0) REVERT: C 406 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: D 283 ARG cc_start: 0.7634 (ttp-170) cc_final: 0.7367 (ttp-170) REVERT: D 501 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8139 (mmt90) outliers start: 17 outliers final: 6 residues processed: 160 average time/residue: 1.7646 time to fit residues: 301.6687 Evaluate side-chains 153 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 417 GLN Chi-restraints excluded: chain C residue 347 ARG Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain D residue 501 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 85 optimal weight: 0.4980 chunk 103 optimal weight: 0.0370 chunk 128 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 145 optimal weight: 0.6980 overall best weight: 1.4460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN C 417 GLN D 254 ASN D 417 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.187481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.125807 restraints weight = 12998.084| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.98 r_work: 0.3229 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14043 Z= 0.138 Angle : 0.539 6.655 19143 Z= 0.286 Chirality : 0.042 0.151 2133 Planarity : 0.005 0.055 2530 Dihedral : 4.330 19.279 1970 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.73 % Favored : 96.21 % Rotamer: Outliers : 1.70 % Allowed : 9.19 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1741 helix: 2.02 (0.21), residues: 677 sheet: 0.30 (0.24), residues: 420 loop : -0.88 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 120 HIS 0.005 0.001 HIS C 127 PHE 0.021 0.002 PHE A 249 TYR 0.019 0.002 TYR C 150 ARG 0.004 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.04901 ( 698) hydrogen bonds : angle 4.48812 ( 2004) covalent geometry : bond 0.00319 (14043) covalent geometry : angle 0.53902 (19143) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 1.544 Fit side-chains REVERT: A 152 ARG cc_start: 0.6355 (ttp80) cc_final: 0.6029 (ttm170) REVERT: A 428 GLU cc_start: 0.5475 (tp30) cc_final: 0.3836 (tt0) REVERT: B 178 LYS cc_start: 0.7901 (tptm) cc_final: 0.7557 (tptt) REVERT: B 252 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: B 387 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6952 (mm-30) REVERT: B 417 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: C 170 ARG cc_start: 0.7906 (ttt-90) cc_final: 0.7690 (ttt90) REVERT: C 182 THR cc_start: 0.7590 (t) cc_final: 0.7077 (m) REVERT: C 406 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: D 170 ARG cc_start: 0.8281 (ttm-80) cc_final: 0.7814 (ttt-90) REVERT: D 283 ARG cc_start: 0.7621 (ttp-170) cc_final: 0.7324 (ttp-170) REVERT: D 501 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8137 (mmt90) outliers start: 24 outliers final: 13 residues processed: 157 average time/residue: 1.6579 time to fit residues: 279.3546 Evaluate side-chains 160 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 417 GLN Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 347 ARG Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 501 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 145 optimal weight: 6.9990 chunk 36 optimal weight: 0.0770 chunk 164 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 overall best weight: 1.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN C 417 GLN D 254 ASN D 417 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.186761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.124871 restraints weight = 12940.379| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.98 r_work: 0.3224 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14043 Z= 0.152 Angle : 0.554 6.427 19143 Z= 0.293 Chirality : 0.042 0.155 2133 Planarity : 0.005 0.056 2530 Dihedral : 4.379 18.809 1970 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.14 % Favored : 95.81 % Rotamer: Outliers : 2.12 % Allowed : 10.11 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.20), residues: 1741 helix: 1.97 (0.21), residues: 682 sheet: 0.27 (0.24), residues: 420 loop : -0.88 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 120 HIS 0.005 0.001 HIS C 127 PHE 0.021 0.002 PHE C 241 TYR 0.015 0.002 TYR C 150 ARG 0.003 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.05127 ( 698) hydrogen bonds : angle 4.48045 ( 2004) covalent geometry : bond 0.00355 (14043) covalent geometry : angle 0.55350 (19143) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.402 Fit side-chains REVERT: A 152 ARG cc_start: 0.6398 (ttp80) cc_final: 0.6051 (ttm170) REVERT: B 178 LYS cc_start: 0.7969 (tptm) cc_final: 0.7563 (tptt) REVERT: B 252 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7379 (mt-10) REVERT: B 417 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: C 170 ARG cc_start: 0.7920 (ttt-90) cc_final: 0.7694 (ttt90) REVERT: C 182 THR cc_start: 0.7611 (t) cc_final: 0.7102 (m) REVERT: C 299 ARG cc_start: 0.7947 (ttp-110) cc_final: 0.7592 (ttp-110) REVERT: C 406 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: C 501 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7239 (mtt90) REVERT: D 170 ARG cc_start: 0.8280 (ttm-80) cc_final: 0.7825 (ttt-90) REVERT: D 283 ARG cc_start: 0.7618 (ttp-170) cc_final: 0.7338 (ttp-170) REVERT: D 501 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8112 (mmt90) outliers start: 30 outliers final: 16 residues processed: 162 average time/residue: 1.6574 time to fit residues: 287.2923 Evaluate side-chains 163 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 417 GLN Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 501 ARG Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 501 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 101 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 88 optimal weight: 0.0040 chunk 63 optimal weight: 0.0970 chunk 157 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS A 490 ASN B 148 GLN C 417 GLN D 254 ASN D 417 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.188849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127425 restraints weight = 12986.967| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.97 r_work: 0.3253 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14043 Z= 0.111 Angle : 0.497 6.046 19143 Z= 0.263 Chirality : 0.041 0.149 2133 Planarity : 0.005 0.054 2530 Dihedral : 4.149 19.075 1970 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.27 % Rotamer: Outliers : 1.91 % Allowed : 10.68 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.21), residues: 1741 helix: 2.17 (0.21), residues: 676 sheet: 0.38 (0.24), residues: 420 loop : -0.80 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 120 HIS 0.004 0.001 HIS C 127 PHE 0.019 0.002 PHE A 249 TYR 0.010 0.001 TYR A 275 ARG 0.003 0.000 ARG C 347 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 698) hydrogen bonds : angle 4.29187 ( 2004) covalent geometry : bond 0.00248 (14043) covalent geometry : angle 0.49744 (19143) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.365 Fit side-chains REVERT: A 152 ARG cc_start: 0.6403 (ttp80) cc_final: 0.6046 (ttm170) REVERT: A 258 GLN cc_start: 0.5481 (OUTLIER) cc_final: 0.5000 (mp10) REVERT: A 428 GLU cc_start: 0.5489 (tp30) cc_final: 0.3865 (tt0) REVERT: B 178 LYS cc_start: 0.7943 (tptm) cc_final: 0.7535 (tptt) REVERT: B 252 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7337 (mt-10) REVERT: B 254 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.7130 (m-40) REVERT: B 345 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7006 (mptt) REVERT: B 417 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: C 170 ARG cc_start: 0.7872 (ttt-90) cc_final: 0.7661 (ttt90) REVERT: C 182 THR cc_start: 0.7543 (t) cc_final: 0.7028 (m) REVERT: C 299 ARG cc_start: 0.7901 (ttp-110) cc_final: 0.7542 (ttp-110) REVERT: C 406 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: C 501 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7206 (mtt90) REVERT: D 170 ARG cc_start: 0.8317 (ttm-80) cc_final: 0.7837 (ttt-90) REVERT: D 283 ARG cc_start: 0.7615 (ttp-170) cc_final: 0.7300 (ttp-170) REVERT: D 501 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8073 (mmt90) outliers start: 27 outliers final: 12 residues processed: 155 average time/residue: 1.6750 time to fit residues: 278.6737 Evaluate side-chains 159 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 417 GLN Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 501 ARG Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 501 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 130 optimal weight: 10.0000 chunk 141 optimal weight: 0.3980 chunk 62 optimal weight: 4.9990 chunk 107 optimal weight: 0.0060 chunk 121 optimal weight: 0.0470 chunk 147 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS C 417 GLN D 254 ASN D 417 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.191200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.130335 restraints weight = 13236.309| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.98 r_work: 0.3292 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14043 Z= 0.092 Angle : 0.463 6.144 19143 Z= 0.244 Chirality : 0.040 0.142 2133 Planarity : 0.004 0.054 2530 Dihedral : 3.878 18.916 1970 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.45 % Favored : 96.50 % Rotamer: Outliers : 1.77 % Allowed : 11.32 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.21), residues: 1741 helix: 2.24 (0.21), residues: 682 sheet: 0.54 (0.25), residues: 416 loop : -0.69 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 120 HIS 0.004 0.001 HIS D 127 PHE 0.015 0.001 PHE C 249 TYR 0.010 0.001 TYR A 275 ARG 0.005 0.000 ARG C 347 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 698) hydrogen bonds : angle 4.09353 ( 2004) covalent geometry : bond 0.00200 (14043) covalent geometry : angle 0.46299 (19143) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.555 Fit side-chains REVERT: A 258 GLN cc_start: 0.5288 (OUTLIER) cc_final: 0.4898 (mp10) REVERT: A 387 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6043 (mp0) REVERT: A 428 GLU cc_start: 0.5515 (tp30) cc_final: 0.5123 (tp30) REVERT: B 152 ARG cc_start: 0.7497 (mtm180) cc_final: 0.7082 (mtp180) REVERT: B 178 LYS cc_start: 0.7882 (tptm) cc_final: 0.7501 (tptt) REVERT: B 252 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: B 254 ASN cc_start: 0.7415 (OUTLIER) cc_final: 0.7208 (m-40) REVERT: B 345 LYS cc_start: 0.8074 (tmmt) cc_final: 0.6953 (mptt) REVERT: B 417 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: B 540 ARG cc_start: 0.7116 (tpt170) cc_final: 0.6912 (tpt170) REVERT: C 182 THR cc_start: 0.7560 (t) cc_final: 0.7055 (m) REVERT: C 299 ARG cc_start: 0.7836 (ttp-110) cc_final: 0.7522 (ttp-110) REVERT: C 346 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7891 (mt-10) REVERT: C 406 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6577 (mp0) REVERT: C 501 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7175 (mtt90) REVERT: D 170 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.7812 (ttt-90) REVERT: D 283 ARG cc_start: 0.7643 (ttp-170) cc_final: 0.7322 (ttp-170) REVERT: D 501 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.7980 (mmt90) outliers start: 25 outliers final: 9 residues processed: 156 average time/residue: 1.6558 time to fit residues: 277.3339 Evaluate side-chains 154 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 417 GLN Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 501 ARG Chi-restraints excluded: chain D residue 501 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 136 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 140 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN C 417 GLN D 254 ASN D 417 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.187580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.129045 restraints weight = 12953.486| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.45 r_work: 0.3217 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14043 Z= 0.151 Angle : 0.542 5.930 19143 Z= 0.287 Chirality : 0.042 0.154 2133 Planarity : 0.005 0.056 2530 Dihedral : 4.195 18.102 1970 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.15 % Rotamer: Outliers : 2.19 % Allowed : 11.74 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.21), residues: 1741 helix: 2.19 (0.21), residues: 676 sheet: 0.41 (0.24), residues: 418 loop : -0.74 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 120 HIS 0.004 0.001 HIS C 127 PHE 0.022 0.002 PHE C 249 TYR 0.013 0.002 TYR A 275 ARG 0.008 0.000 ARG C 170 Details of bonding type rmsd hydrogen bonds : bond 0.04891 ( 698) hydrogen bonds : angle 4.32868 ( 2004) covalent geometry : bond 0.00354 (14043) covalent geometry : angle 0.54152 (19143) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 1.695 Fit side-chains REVERT: A 258 GLN cc_start: 0.5413 (OUTLIER) cc_final: 0.4956 (mp10) REVERT: A 307 SER cc_start: 0.5369 (p) cc_final: 0.4986 (t) REVERT: A 387 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.6034 (mp0) REVERT: A 428 GLU cc_start: 0.5436 (tp30) cc_final: 0.4972 (tp30) REVERT: A 533 GLN cc_start: 0.5177 (mp10) cc_final: 0.4667 (pm20) REVERT: B 178 LYS cc_start: 0.7803 (tptm) cc_final: 0.7407 (tptt) REVERT: B 252 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7269 (mt-10) REVERT: B 345 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.6973 (mptt) REVERT: B 417 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8025 (tt0) REVERT: C 133 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8299 (m-30) REVERT: C 182 THR cc_start: 0.7497 (t) cc_final: 0.6991 (m) REVERT: C 299 ARG cc_start: 0.7846 (ttp-110) cc_final: 0.7493 (ttp-110) REVERT: C 406 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: C 501 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7084 (mtt90) REVERT: D 170 ARG cc_start: 0.8256 (ttm-80) cc_final: 0.7732 (ttt-90) REVERT: D 283 ARG cc_start: 0.7552 (ttp-170) cc_final: 0.7223 (ttp-170) REVERT: D 501 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8049 (mmt90) outliers start: 31 outliers final: 15 residues processed: 160 average time/residue: 1.6470 time to fit residues: 283.5568 Evaluate side-chains 164 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TRP Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 417 GLN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 501 ARG Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 501 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 83 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN C 417 GLN D 254 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.188771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.130152 restraints weight = 13007.098| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.31 r_work: 0.3236 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14043 Z= 0.116 Angle : 0.504 6.028 19143 Z= 0.267 Chirality : 0.041 0.151 2133 Planarity : 0.005 0.056 2530 Dihedral : 4.093 18.594 1970 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.32 % Rotamer: Outliers : 2.05 % Allowed : 12.23 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1741 helix: 2.23 (0.21), residues: 676 sheet: 0.43 (0.24), residues: 418 loop : -0.72 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 120 HIS 0.004 0.001 HIS C 127 PHE 0.018 0.002 PHE C 249 TYR 0.011 0.001 TYR A 275 ARG 0.002 0.000 ARG B 540 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 698) hydrogen bonds : angle 4.24521 ( 2004) covalent geometry : bond 0.00264 (14043) covalent geometry : angle 0.50438 (19143) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 1.504 Fit side-chains REVERT: A 258 GLN cc_start: 0.5345 (OUTLIER) cc_final: 0.4899 (mp10) REVERT: A 307 SER cc_start: 0.5353 (p) cc_final: 0.4969 (t) REVERT: A 387 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.6004 (mp0) REVERT: A 428 GLU cc_start: 0.5529 (tp30) cc_final: 0.5122 (tp30) REVERT: A 533 GLN cc_start: 0.5126 (mp10) cc_final: 0.4624 (pm20) REVERT: B 178 LYS cc_start: 0.7770 (tptm) cc_final: 0.7476 (tptt) REVERT: B 252 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: B 345 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.6987 (mptt) REVERT: B 417 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: C 133 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8235 (m-30) REVERT: C 170 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7537 (ttt90) REVERT: C 182 THR cc_start: 0.7533 (t) cc_final: 0.7026 (m) REVERT: C 299 ARG cc_start: 0.7846 (ttp-110) cc_final: 0.7487 (ttp-110) REVERT: C 406 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: C 501 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7117 (mtt90) REVERT: D 170 ARG cc_start: 0.8268 (ttm-80) cc_final: 0.7752 (ttt-90) REVERT: D 283 ARG cc_start: 0.7600 (ttp-170) cc_final: 0.7288 (ttp-170) REVERT: D 501 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8062 (mmt90) outliers start: 29 outliers final: 14 residues processed: 157 average time/residue: 1.7052 time to fit residues: 287.3577 Evaluate side-chains 162 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 417 GLN Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 501 ARG Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 501 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 111 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 172 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN C 417 GLN D 254 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.189423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.131719 restraints weight = 12956.954| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.31 r_work: 0.3259 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14043 Z= 0.109 Angle : 0.493 6.038 19143 Z= 0.261 Chirality : 0.040 0.149 2133 Planarity : 0.005 0.055 2530 Dihedral : 4.015 18.622 1970 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.73 % Favored : 96.21 % Rotamer: Outliers : 1.98 % Allowed : 12.31 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.21), residues: 1741 helix: 2.20 (0.21), residues: 682 sheet: 0.50 (0.25), residues: 414 loop : -0.70 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 120 HIS 0.004 0.001 HIS C 127 PHE 0.018 0.002 PHE C 249 TYR 0.010 0.001 TYR A 275 ARG 0.002 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 698) hydrogen bonds : angle 4.18244 ( 2004) covalent geometry : bond 0.00247 (14043) covalent geometry : angle 0.49314 (19143) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.600 Fit side-chains REVERT: A 258 GLN cc_start: 0.5347 (OUTLIER) cc_final: 0.4988 (mp10) REVERT: A 307 SER cc_start: 0.5382 (p) cc_final: 0.5007 (t) REVERT: A 370 ARG cc_start: 0.5390 (mtp85) cc_final: 0.5085 (mtp180) REVERT: A 387 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6106 (mp0) REVERT: A 428 GLU cc_start: 0.5563 (tp30) cc_final: 0.5242 (tp30) REVERT: A 533 GLN cc_start: 0.5124 (mp10) cc_final: 0.4614 (pm20) REVERT: B 178 LYS cc_start: 0.7812 (tptm) cc_final: 0.7519 (tptt) REVERT: B 252 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7279 (mt-10) REVERT: B 345 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7012 (mptt) REVERT: B 417 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: C 133 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8209 (m-30) REVERT: C 182 THR cc_start: 0.7553 (t) cc_final: 0.7061 (m) REVERT: C 299 ARG cc_start: 0.7866 (ttp-110) cc_final: 0.7494 (ttp-110) REVERT: C 406 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: C 501 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7074 (mtt90) REVERT: D 170 ARG cc_start: 0.8255 (ttm-80) cc_final: 0.7739 (ttt-90) REVERT: D 283 ARG cc_start: 0.7615 (ttp-170) cc_final: 0.7288 (ttp-170) REVERT: D 501 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8063 (mmt90) outliers start: 28 outliers final: 14 residues processed: 158 average time/residue: 1.6487 time to fit residues: 280.4767 Evaluate side-chains 164 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 417 GLN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 501 ARG Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 501 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 29 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 160 optimal weight: 0.0970 chunk 144 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 115 optimal weight: 0.0970 chunk 65 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.9978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN C 417 GLN D 254 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.189277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.130872 restraints weight = 13011.984| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.59 r_work: 0.3210 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14043 Z= 0.112 Angle : 0.499 6.041 19143 Z= 0.264 Chirality : 0.041 0.151 2133 Planarity : 0.005 0.055 2530 Dihedral : 4.016 18.353 1970 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.27 % Rotamer: Outliers : 1.63 % Allowed : 12.80 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.21), residues: 1741 helix: 2.20 (0.21), residues: 682 sheet: 0.50 (0.24), residues: 414 loop : -0.69 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 120 HIS 0.004 0.001 HIS D 127 PHE 0.018 0.002 PHE C 249 TYR 0.010 0.001 TYR A 275 ARG 0.004 0.000 ARG C 170 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 698) hydrogen bonds : angle 4.19275 ( 2004) covalent geometry : bond 0.00253 (14043) covalent geometry : angle 0.49892 (19143) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3482 Ramachandran restraints generated. 1741 Oldfield, 0 Emsley, 1741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.476 Fit side-chains REVERT: A 137 MET cc_start: 0.7425 (ttp) cc_final: 0.7000 (ptm) REVERT: A 152 ARG cc_start: 0.6413 (ttp-170) cc_final: 0.5972 (ttm170) REVERT: A 258 GLN cc_start: 0.5322 (OUTLIER) cc_final: 0.4875 (mp10) REVERT: A 307 SER cc_start: 0.5297 (p) cc_final: 0.4945 (t) REVERT: A 381 ARG cc_start: 0.5645 (mtp180) cc_final: 0.5441 (mtp180) REVERT: A 387 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6089 (mp0) REVERT: A 428 GLU cc_start: 0.5520 (tp30) cc_final: 0.5198 (tp30) REVERT: A 533 GLN cc_start: 0.5121 (mp10) cc_final: 0.4616 (pm20) REVERT: B 178 LYS cc_start: 0.7736 (tptm) cc_final: 0.7456 (tptt) REVERT: B 252 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7299 (mt-10) REVERT: B 345 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.6949 (mptt) REVERT: B 417 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: C 133 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8255 (m-30) REVERT: C 170 ARG cc_start: 0.7821 (ttt-90) cc_final: 0.7569 (ttt90) REVERT: C 182 THR cc_start: 0.7490 (t) cc_final: 0.6987 (m) REVERT: C 299 ARG cc_start: 0.7840 (ttp-110) cc_final: 0.7461 (ttp-110) REVERT: C 406 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6763 (mp0) REVERT: C 501 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7112 (mtt90) REVERT: D 170 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7701 (ttt-90) REVERT: D 283 ARG cc_start: 0.7564 (ttp-170) cc_final: 0.7234 (ttp-170) REVERT: D 501 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8074 (mmt90) outliers start: 23 outliers final: 14 residues processed: 154 average time/residue: 1.6728 time to fit residues: 276.2555 Evaluate side-chains 162 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 TYR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 417 GLN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 501 ARG Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 498 ASP Chi-restraints excluded: chain D residue 501 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 24 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN C 417 GLN D 254 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.187484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128600 restraints weight = 12988.690| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.48 r_work: 0.3186 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14043 Z= 0.148 Angle : 0.546 5.943 19143 Z= 0.289 Chirality : 0.042 0.156 2133 Planarity : 0.005 0.057 2530 Dihedral : 4.225 18.708 1970 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.85 % Favored : 96.04 % Rotamer: Outliers : 2.05 % Allowed : 12.45 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.21), residues: 1741 helix: 2.16 (0.21), residues: 677 sheet: 0.43 (0.24), residues: 416 loop : -0.75 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 120 HIS 0.004 0.001 HIS C 127 PHE 0.022 0.002 PHE C 249 TYR 0.012 0.002 TYR C 168 ARG 0.003 0.000 ARG C 262 Details of bonding type rmsd hydrogen bonds : bond 0.04900 ( 698) hydrogen bonds : angle 4.32511 ( 2004) covalent geometry : bond 0.00347 (14043) covalent geometry : angle 0.54575 (19143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13003.63 seconds wall clock time: 220 minutes 50.39 seconds (13250.39 seconds total)