Starting phenix.real_space_refine on Thu Jul 24 19:23:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dlf_46976/07_2025/9dlf_46976_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dlf_46976/07_2025/9dlf_46976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dlf_46976/07_2025/9dlf_46976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dlf_46976/07_2025/9dlf_46976.map" model { file = "/net/cci-nas-00/data/ceres_data/9dlf_46976/07_2025/9dlf_46976_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dlf_46976/07_2025/9dlf_46976_neut.cif" } resolution = 2.85 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= 0.063 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 28 5.16 5 C 4263 2.51 5 N 1121 2.21 5 O 1167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6580 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 4744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4744 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 42, 'TRANS': 574} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 820 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 100} Chain: "B" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 967 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.25, per 1000 atoms: 0.80 Number of scatterers: 6580 At special positions: 0 Unit cell: (79.17, 97.44, 126.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 1 15.00 O 1167 8.00 N 1121 7.00 C 4263 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 88 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 1.6 seconds 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1542 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 8 sheets defined 48.0% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'C' and resid 31 through 55 removed outlier: 3.719A pdb=" N LEU C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 75 removed outlier: 4.207A pdb=" N VAL C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU C 67 " --> pdb=" O GLY C 63 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR C 69 " --> pdb=" O ILE C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 106 Processing helix chain 'C' and resid 111 through 139 removed outlier: 3.582A pdb=" N ARG C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 137 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 143 removed outlier: 4.004A pdb=" N THR C 143 " --> pdb=" O PRO C 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 140 through 143' Processing helix chain 'C' and resid 152 through 160 removed outlier: 3.682A pdb=" N VAL C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE C 160 " --> pdb=" O VAL C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 166 removed outlier: 3.549A pdb=" N ARG C 164 " --> pdb=" O ILE C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 193 Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 216 through 221 removed outlier: 3.716A pdb=" N VAL C 220 " --> pdb=" O MET C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 removed outlier: 3.611A pdb=" N LEU C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 253 removed outlier: 3.670A pdb=" N ARG C 245 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY C 253 " --> pdb=" O VAL C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 268 removed outlier: 3.611A pdb=" N VAL C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 278 removed outlier: 3.766A pdb=" N LYS C 278 " --> pdb=" O THR C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 297 Processing helix chain 'C' and resid 301 through 320 removed outlier: 3.718A pdb=" N ALA C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 318 " --> pdb=" O MET C 314 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG C 319 " --> pdb=" O VAL C 315 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 342 through 365 removed outlier: 3.767A pdb=" N VAL C 346 " --> pdb=" O SER C 342 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL C 347 " --> pdb=" O PRO C 343 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 374 through 382 removed outlier: 3.879A pdb=" N LEU C 378 " --> pdb=" O LEU C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 385 No H-bonds generated for 'chain 'C' and resid 383 through 385' Processing helix chain 'C' and resid 400 through 426 removed outlier: 3.546A pdb=" N LEU C 405 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR C 406 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY C 408 " --> pdb=" O TYR C 404 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR C 410 " --> pdb=" O TYR C 406 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN C 426 " --> pdb=" O LEU C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 453 Processing helix chain 'C' and resid 462 through 467 removed outlier: 3.641A pdb=" N LEU C 465 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP C 466 " --> pdb=" O ASP C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 479 removed outlier: 4.237A pdb=" N LEU C 474 " --> pdb=" O MET C 470 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR C 475 " --> pdb=" O ARG C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 534 removed outlier: 3.643A pdb=" N ASN C 532 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLY C 534 " --> pdb=" O GLY C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 553 removed outlier: 3.869A pdb=" N THR C 553 " --> pdb=" O ALA C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 575 removed outlier: 3.981A pdb=" N ALA C 572 " --> pdb=" O PHE C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 removed outlier: 3.655A pdb=" N ILE C 585 " --> pdb=" O PRO C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 601 Processing helix chain 'C' and resid 603 through 613 removed outlier: 3.526A pdb=" N LYS C 608 " --> pdb=" O PRO C 604 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 609 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE C 613 " --> pdb=" O VAL C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 628 removed outlier: 3.634A pdb=" N PHE C 622 " --> pdb=" O GLY C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 634 Processing helix chain 'C' and resid 640 through 649 Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.339A pdb=" N PHE A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 147 through 151 Processing sheet with id=AA2, first strand: chain 'C' and resid 495 through 499 removed outlier: 6.101A pdb=" N ALA C 484 " --> pdb=" O THR C 520 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE C 522 " --> pdb=" O ALA C 484 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU C 486 " --> pdb=" O PHE C 522 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.539A pdb=" N ALA A 12 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.539A pdb=" N ALA A 12 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 7 removed outlier: 4.480A pdb=" N GLY B 16 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU B 18 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ASN B 84 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B 20 " --> pdb=" O GLN B 82 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLN B 82 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N CYS B 22 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N TYR B 80 " --> pdb=" O CYS B 22 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ALA B 24 " --> pdb=" O THR B 78 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR B 78 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 57 through 60 removed outlier: 6.746A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE B 34 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N CYS B 96 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TRP B 115 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG B 98 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ALA B 111 " --> pdb=" O TYR B 100 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 57 through 60 removed outlier: 6.746A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE B 34 " --> pdb=" O SER B 50 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 900 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: 2.14 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1029 1.32 - 1.44: 1915 1.44 - 1.57: 3763 1.57 - 1.69: 3 1.69 - 1.82: 48 Bond restraints: 6758 Sorted by residual: bond pdb=" N ILE C 540 " pdb=" CA ILE C 540 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.15e-02 7.56e+03 1.67e+01 bond pdb=" CA MET C 216 " pdb=" C MET C 216 " ideal model delta sigma weight residual 1.522 1.578 -0.056 1.72e-02 3.38e+03 1.06e+01 bond pdb=" C ILE C 540 " pdb=" O ILE C 540 " ideal model delta sigma weight residual 1.235 1.207 0.028 1.05e-02 9.07e+03 7.27e+00 bond pdb=" N VAL C 539 " pdb=" CA VAL C 539 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.24e-02 6.50e+03 5.92e+00 bond pdb=" N GLU C 644 " pdb=" CA GLU C 644 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 5.11e+00 ... (remaining 6753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 8965 1.74 - 3.47: 217 3.47 - 5.21: 33 5.21 - 6.94: 9 6.94 - 8.68: 1 Bond angle restraints: 9225 Sorted by residual: angle pdb=" N PRO C 582 " pdb=" CA PRO C 582 " pdb=" C PRO C 582 " ideal model delta sigma weight residual 110.70 115.20 -4.50 1.22e+00 6.72e-01 1.36e+01 angle pdb=" CA HIS C 563 " pdb=" C HIS C 563 " pdb=" O HIS C 563 " ideal model delta sigma weight residual 121.78 117.91 3.87 1.12e+00 7.97e-01 1.20e+01 angle pdb=" CA ILE C 540 " pdb=" C ILE C 540 " pdb=" O ILE C 540 " ideal model delta sigma weight residual 121.32 116.98 4.34 1.32e+00 5.74e-01 1.08e+01 angle pdb=" CA VAL C 539 " pdb=" C VAL C 539 " pdb=" N ILE C 540 " ideal model delta sigma weight residual 116.34 120.38 -4.04 1.28e+00 6.10e-01 9.94e+00 angle pdb=" N GLU C 644 " pdb=" CA GLU C 644 " pdb=" C GLU C 644 " ideal model delta sigma weight residual 110.97 107.56 3.41 1.09e+00 8.42e-01 9.81e+00 ... (remaining 9220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.71: 3764 25.71 - 51.42: 152 51.42 - 77.13: 16 77.13 - 102.84: 9 102.84 - 128.56: 5 Dihedral angle restraints: 3946 sinusoidal: 1513 harmonic: 2433 Sorted by residual: dihedral pdb=" C37 6OU C 701 " pdb=" C38 6OU C 701 " pdb=" C39 6OU C 701 " pdb=" C40 6OU C 701 " ideal model delta sinusoidal sigma weight residual 178.01 49.45 128.56 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C12 6OU C 701 " pdb=" C13 6OU C 701 " pdb=" C14 6OU C 701 " pdb=" C15 6OU C 701 " ideal model delta sinusoidal sigma weight residual 186.47 64.58 121.89 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 88 " pdb=" CB CYS A 88 " ideal model delta sinusoidal sigma weight residual 93.00 60.36 32.64 1 1.00e+01 1.00e-02 1.52e+01 ... (remaining 3943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 784 0.046 - 0.092: 187 0.092 - 0.137: 46 0.137 - 0.183: 8 0.183 - 0.229: 3 Chirality restraints: 1028 Sorted by residual: chirality pdb=" CA LYS C 278 " pdb=" N LYS C 278 " pdb=" C LYS C 278 " pdb=" CB LYS C 278 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ILE C 540 " pdb=" N ILE C 540 " pdb=" C ILE C 540 " pdb=" CB ILE C 540 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA GLN C 297 " pdb=" N GLN C 297 " pdb=" C GLN C 297 " pdb=" CB GLN C 297 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.15e-01 ... (remaining 1025 not shown) Planarity restraints: 1164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C39 6OU C 701 " 0.098 2.00e-02 2.50e+03 2.39e-01 5.73e+02 pdb=" C40 6OU C 701 " -0.320 2.00e-02 2.50e+03 pdb=" C41 6OU C 701 " 0.326 2.00e-02 2.50e+03 pdb=" C42 6OU C 701 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 427 " -0.061 5.00e-02 4.00e+02 9.10e-02 1.32e+01 pdb=" N PRO C 428 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO C 428 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 428 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 297 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO C 298 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 298 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 298 " -0.038 5.00e-02 4.00e+02 ... (remaining 1161 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 641 2.75 - 3.29: 5930 3.29 - 3.82: 10049 3.82 - 4.36: 11972 4.36 - 4.90: 21331 Nonbonded interactions: 49923 Sorted by model distance: nonbonded pdb=" O ARG C 447 " pdb=" NE2 GLN C 451 " model vdw 2.211 3.120 nonbonded pdb=" O MET C 314 " pdb=" OH TYR C 406 " model vdw 2.235 3.040 nonbonded pdb=" NH2 ARG C 201 " pdb=" O ALA C 238 " model vdw 2.285 3.120 nonbonded pdb=" OD2 ASP C 496 " pdb=" OH TYR C 588 " model vdw 2.289 3.040 nonbonded pdb=" CD1 LEU C 355 " pdb=" C46 6OU C 701 " model vdw 2.302 3.860 ... (remaining 49918 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.980 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 0.008 0.576 6760 Z= 0.729 Angle : 0.649 8.680 9227 Z= 0.358 Chirality : 0.045 0.229 1028 Planarity : 0.010 0.239 1164 Dihedral : 14.906 128.556 2401 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -0.12 (0.29), residues: 844 helix: 1.04 (0.29), residues: 352 sheet: 0.51 (0.47), residues: 140 loop : -1.50 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 33 HIS 0.006 0.001 HIS C 563 PHE 0.025 0.002 PHE C 49 TYR 0.040 0.002 TYR B 100 ARG 0.007 0.001 ARG C 494 Details of bonding type rmsd hydrogen bonds : bond 0.18537 ( 303) hydrogen bonds : angle 6.64933 ( 900) SS BOND : bond 0.00844 ( 1) SS BOND : angle 1.57840 ( 2) covalent geometry : bond 0.00389 ( 6758) covalent geometry : angle 0.64907 ( 9225) Misc. bond : bond 0.57578 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.734 Fit side-chains REVERT: C 398 MET cc_start: 0.5625 (mmt) cc_final: 0.5248 (mtp) REVERT: B 90 ASP cc_start: 0.7753 (m-30) cc_final: 0.7397 (m-30) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 1.1605 time to fit residues: 132.3906 Evaluate side-chains 89 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.4980 chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.145365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.123384 restraints weight = 7049.078| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.42 r_work: 0.3183 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6760 Z= 0.152 Angle : 0.597 6.408 9227 Z= 0.309 Chirality : 0.043 0.154 1028 Planarity : 0.006 0.055 1164 Dihedral : 12.751 168.143 991 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.83 % Allowed : 6.26 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.13 (0.29), residues: 844 helix: 1.38 (0.28), residues: 356 sheet: 0.62 (0.47), residues: 145 loop : -1.59 (0.29), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 33 HIS 0.007 0.001 HIS C 31 PHE 0.012 0.001 PHE C 349 TYR 0.017 0.002 TYR C 259 ARG 0.005 0.000 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.06566 ( 303) hydrogen bonds : angle 4.32999 ( 900) SS BOND : bond 0.01219 ( 1) SS BOND : angle 2.09368 ( 2) covalent geometry : bond 0.00338 ( 6758) covalent geometry : angle 0.59627 ( 9225) Misc. bond : bond 0.00149 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.736 Fit side-chains REVERT: C 287 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7320 (mt0) REVERT: C 398 MET cc_start: 0.6311 (mmt) cc_final: 0.5625 (mtp) REVERT: C 478 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: C 479 ASN cc_start: 0.8588 (m-40) cc_final: 0.8173 (m-40) REVERT: C 644 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7625 (tm-30) REVERT: B 28 ASN cc_start: 0.9106 (m-40) cc_final: 0.8893 (m110) REVERT: B 58 THR cc_start: 0.8855 (m) cc_final: 0.8647 (t) REVERT: B 90 ASP cc_start: 0.8124 (m-30) cc_final: 0.7839 (m-30) outliers start: 19 outliers final: 9 residues processed: 91 average time/residue: 1.1246 time to fit residues: 108.2927 Evaluate side-chains 91 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain B residue 12 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.0270 chunk 52 optimal weight: 0.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.147825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.125779 restraints weight = 7080.431| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.51 r_work: 0.3212 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6760 Z= 0.116 Angle : 0.522 5.917 9227 Z= 0.269 Chirality : 0.040 0.142 1028 Planarity : 0.005 0.043 1164 Dihedral : 11.260 132.905 991 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.68 % Allowed : 7.60 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.46 (0.29), residues: 844 helix: 1.79 (0.29), residues: 353 sheet: 0.77 (0.47), residues: 144 loop : -1.54 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 33 HIS 0.002 0.001 HIS C 31 PHE 0.009 0.001 PHE C 349 TYR 0.016 0.001 TYR C 259 ARG 0.004 0.000 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.05186 ( 303) hydrogen bonds : angle 3.89092 ( 900) SS BOND : bond 0.00945 ( 1) SS BOND : angle 1.67039 ( 2) covalent geometry : bond 0.00250 ( 6758) covalent geometry : angle 0.52189 ( 9225) Misc. bond : bond 0.00086 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.670 Fit side-chains REVERT: C 146 ARG cc_start: 0.7499 (mmt-90) cc_final: 0.7257 (mmt-90) REVERT: C 287 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7369 (mt0) REVERT: C 314 MET cc_start: 0.8048 (ttp) cc_final: 0.7692 (ttt) REVERT: C 317 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6291 (mp) REVERT: C 336 ILE cc_start: 0.8207 (mp) cc_final: 0.7948 (mm) REVERT: C 398 MET cc_start: 0.6354 (mmt) cc_final: 0.5687 (mtp) REVERT: C 404 TYR cc_start: 0.6694 (m-10) cc_final: 0.6442 (m-10) REVERT: C 444 ASP cc_start: 0.7727 (t70) cc_final: 0.7443 (t70) REVERT: C 479 ASN cc_start: 0.8539 (m-40) cc_final: 0.8188 (m-40) REVERT: C 644 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: B 58 THR cc_start: 0.8779 (m) cc_final: 0.8577 (t) REVERT: B 90 ASP cc_start: 0.8161 (m-30) cc_final: 0.7912 (m-30) outliers start: 18 outliers final: 8 residues processed: 93 average time/residue: 1.1905 time to fit residues: 117.5206 Evaluate side-chains 89 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain B residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 0.0370 overall best weight: 0.4460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.150107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.128143 restraints weight = 7179.743| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.49 r_work: 0.3253 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6760 Z= 0.104 Angle : 0.494 6.568 9227 Z= 0.252 Chirality : 0.040 0.145 1028 Planarity : 0.005 0.044 1164 Dihedral : 10.140 103.076 991 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.68 % Allowed : 8.79 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.66 (0.30), residues: 844 helix: 1.96 (0.29), residues: 360 sheet: 1.12 (0.48), residues: 138 loop : -1.59 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 33 HIS 0.002 0.000 HIS C 31 PHE 0.009 0.001 PHE C 349 TYR 0.016 0.001 TYR C 259 ARG 0.005 0.000 ARG C 145 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 303) hydrogen bonds : angle 3.60868 ( 900) SS BOND : bond 0.00810 ( 1) SS BOND : angle 1.43763 ( 2) covalent geometry : bond 0.00221 ( 6758) covalent geometry : angle 0.49398 ( 9225) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.732 Fit side-chains REVERT: C 110 ARG cc_start: 0.6288 (mtt90) cc_final: 0.5839 (ttt180) REVERT: C 146 ARG cc_start: 0.7375 (mmt-90) cc_final: 0.7164 (mmt-90) REVERT: C 287 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7322 (mt0) REVERT: C 336 ILE cc_start: 0.8155 (mp) cc_final: 0.7897 (mm) REVERT: C 398 MET cc_start: 0.6194 (mmt) cc_final: 0.5647 (mtm) REVERT: C 444 ASP cc_start: 0.7585 (t70) cc_final: 0.7295 (t70) REVERT: C 451 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6708 (mp10) REVERT: C 479 ASN cc_start: 0.8479 (m-40) cc_final: 0.8140 (m-40) REVERT: C 644 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7611 (tm-30) REVERT: A 90 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: B 43 LYS cc_start: 0.8356 (mptp) cc_final: 0.8107 (mptp) REVERT: B 58 THR cc_start: 0.8782 (m) cc_final: 0.8562 (t) REVERT: B 90 ASP cc_start: 0.8090 (m-30) cc_final: 0.7841 (m-30) outliers start: 18 outliers final: 7 residues processed: 94 average time/residue: 1.1297 time to fit residues: 112.3265 Evaluate side-chains 90 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain B residue 12 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 43 optimal weight: 0.0270 chunk 3 optimal weight: 0.0470 chunk 72 optimal weight: 0.6980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.150240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.127904 restraints weight = 7073.962| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.51 r_work: 0.3251 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6760 Z= 0.102 Angle : 0.495 6.090 9227 Z= 0.250 Chirality : 0.039 0.142 1028 Planarity : 0.005 0.044 1164 Dihedral : 9.701 102.599 991 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.09 % Allowed : 10.43 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 (0.30), residues: 844 helix: 2.09 (0.29), residues: 358 sheet: 1.19 (0.48), residues: 138 loop : -1.52 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 184 HIS 0.007 0.001 HIS C 563 PHE 0.009 0.001 PHE C 349 TYR 0.015 0.001 TYR C 259 ARG 0.003 0.000 ARG C 145 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 303) hydrogen bonds : angle 3.47807 ( 900) SS BOND : bond 0.00841 ( 1) SS BOND : angle 1.57262 ( 2) covalent geometry : bond 0.00219 ( 6758) covalent geometry : angle 0.49439 ( 9225) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.835 Fit side-chains REVERT: C 35 ARG cc_start: 0.8114 (tpp80) cc_final: 0.7720 (tpp-160) REVERT: C 110 ARG cc_start: 0.6296 (mtt90) cc_final: 0.5792 (ttt180) REVERT: C 146 ARG cc_start: 0.7499 (mmt-90) cc_final: 0.7267 (mmt-90) REVERT: C 284 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8063 (mttp) REVERT: C 287 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7324 (mt0) REVERT: C 314 MET cc_start: 0.8082 (ttp) cc_final: 0.7678 (ttt) REVERT: C 336 ILE cc_start: 0.8191 (mp) cc_final: 0.7927 (mm) REVERT: C 398 MET cc_start: 0.6163 (mmt) cc_final: 0.5571 (mtm) REVERT: C 444 ASP cc_start: 0.7599 (t70) cc_final: 0.7277 (t70) REVERT: C 451 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.6728 (mp10) REVERT: C 479 ASN cc_start: 0.8481 (m-40) cc_final: 0.8146 (m-40) REVERT: C 644 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: B 43 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8112 (mptp) REVERT: B 90 ASP cc_start: 0.8013 (m-30) cc_final: 0.7729 (m-30) outliers start: 14 outliers final: 8 residues processed: 92 average time/residue: 1.2611 time to fit residues: 122.9859 Evaluate side-chains 94 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 39 optimal weight: 0.0370 chunk 76 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.147351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.124945 restraints weight = 7005.830| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.50 r_work: 0.3218 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6760 Z= 0.123 Angle : 0.529 6.054 9227 Z= 0.270 Chirality : 0.040 0.155 1028 Planarity : 0.005 0.042 1164 Dihedral : 9.533 100.378 991 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.68 % Allowed : 10.73 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.64 (0.30), residues: 844 helix: 1.93 (0.29), residues: 361 sheet: 0.77 (0.47), residues: 147 loop : -1.49 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 115 HIS 0.002 0.001 HIS C 552 PHE 0.011 0.001 PHE C 349 TYR 0.016 0.001 TYR C 259 ARG 0.004 0.000 ARG C 595 Details of bonding type rmsd hydrogen bonds : bond 0.05260 ( 303) hydrogen bonds : angle 3.56275 ( 900) SS BOND : bond 0.00997 ( 1) SS BOND : angle 1.89630 ( 2) covalent geometry : bond 0.00275 ( 6758) covalent geometry : angle 0.52783 ( 9225) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.718 Fit side-chains REVERT: C 35 ARG cc_start: 0.8146 (tpp80) cc_final: 0.7760 (tpp-160) REVERT: C 110 ARG cc_start: 0.6330 (mtt90) cc_final: 0.5827 (ttt180) REVERT: C 284 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8074 (mttp) REVERT: C 287 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7351 (mt0) REVERT: C 336 ILE cc_start: 0.8254 (mp) cc_final: 0.7967 (mm) REVERT: C 398 MET cc_start: 0.6383 (mmt) cc_final: 0.5725 (mtp) REVERT: C 404 TYR cc_start: 0.6488 (m-10) cc_final: 0.6216 (m-10) REVERT: C 479 ASN cc_start: 0.8482 (m-40) cc_final: 0.8137 (m-40) REVERT: C 644 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7640 (tm-30) REVERT: A 45 LYS cc_start: 0.8239 (mptt) cc_final: 0.7541 (mmtm) REVERT: B 43 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8147 (mptp) REVERT: B 90 ASP cc_start: 0.8015 (m-30) cc_final: 0.7770 (m-30) outliers start: 18 outliers final: 10 residues processed: 96 average time/residue: 1.2014 time to fit residues: 121.7473 Evaluate side-chains 97 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 66 optimal weight: 0.0470 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.148116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.126086 restraints weight = 7122.654| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.48 r_work: 0.3229 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6760 Z= 0.113 Angle : 0.511 6.102 9227 Z= 0.260 Chirality : 0.040 0.149 1028 Planarity : 0.005 0.043 1164 Dihedral : 9.399 102.273 991 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.53 % Allowed : 11.62 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.69 (0.30), residues: 844 helix: 2.00 (0.29), residues: 360 sheet: 0.79 (0.47), residues: 147 loop : -1.47 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 33 HIS 0.008 0.001 HIS C 563 PHE 0.010 0.001 PHE C 349 TYR 0.016 0.001 TYR C 259 ARG 0.004 0.000 ARG C 146 Details of bonding type rmsd hydrogen bonds : bond 0.04858 ( 303) hydrogen bonds : angle 3.50734 ( 900) SS BOND : bond 0.00891 ( 1) SS BOND : angle 1.74020 ( 2) covalent geometry : bond 0.00248 ( 6758) covalent geometry : angle 0.51051 ( 9225) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.711 Fit side-chains REVERT: C 35 ARG cc_start: 0.8131 (tpp80) cc_final: 0.7755 (tpp-160) REVERT: C 110 ARG cc_start: 0.6321 (mtt90) cc_final: 0.5829 (ttt180) REVERT: C 284 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8087 (mttp) REVERT: C 287 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7372 (mt0) REVERT: C 336 ILE cc_start: 0.8243 (mp) cc_final: 0.7959 (mm) REVERT: C 398 MET cc_start: 0.6300 (mmt) cc_final: 0.5709 (mtp) REVERT: C 404 TYR cc_start: 0.6497 (m-10) cc_final: 0.6189 (m-10) REVERT: C 479 ASN cc_start: 0.8445 (m-40) cc_final: 0.8103 (m-40) REVERT: C 595 ARG cc_start: 0.8114 (ttp-170) cc_final: 0.7909 (ttp-170) REVERT: C 644 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: A 77 SER cc_start: 0.7325 (OUTLIER) cc_final: 0.6851 (t) REVERT: A 90 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7979 (tp40) REVERT: B 43 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8156 (mptp) outliers start: 17 outliers final: 10 residues processed: 95 average time/residue: 1.1824 time to fit residues: 118.5678 Evaluate side-chains 99 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 48 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.143826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.121271 restraints weight = 7068.243| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.51 r_work: 0.3166 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6760 Z= 0.161 Angle : 0.597 6.606 9227 Z= 0.306 Chirality : 0.042 0.162 1028 Planarity : 0.006 0.044 1164 Dihedral : 9.657 100.029 991 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.38 % Allowed : 12.52 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.48 (0.29), residues: 844 helix: 1.76 (0.28), residues: 361 sheet: 0.69 (0.47), residues: 148 loop : -1.54 (0.29), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 115 HIS 0.005 0.001 HIS C 563 PHE 0.012 0.001 PHE C 349 TYR 0.018 0.002 TYR C 259 ARG 0.008 0.001 ARG C 146 Details of bonding type rmsd hydrogen bonds : bond 0.06538 ( 303) hydrogen bonds : angle 3.71958 ( 900) SS BOND : bond 0.01167 ( 1) SS BOND : angle 2.27925 ( 2) covalent geometry : bond 0.00370 ( 6758) covalent geometry : angle 0.59602 ( 9225) Misc. bond : bond 0.00069 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.715 Fit side-chains REVERT: C 35 ARG cc_start: 0.8246 (tpp80) cc_final: 0.7883 (tpp-160) REVERT: C 146 ARG cc_start: 0.7604 (mmt-90) cc_final: 0.7354 (mmt180) REVERT: C 284 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8170 (mttp) REVERT: C 287 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7503 (mt0) REVERT: C 336 ILE cc_start: 0.8335 (mp) cc_final: 0.8096 (mm) REVERT: C 398 MET cc_start: 0.6503 (mmt) cc_final: 0.5871 (mtp) REVERT: C 404 TYR cc_start: 0.6671 (m-10) cc_final: 0.6454 (m-10) REVERT: C 479 ASN cc_start: 0.8479 (m-40) cc_final: 0.8154 (m-40) REVERT: C 644 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: B 43 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8225 (mptp) REVERT: B 62 ASP cc_start: 0.7719 (m-30) cc_final: 0.7479 (m-30) outliers start: 16 outliers final: 10 residues processed: 99 average time/residue: 1.2364 time to fit residues: 128.7981 Evaluate side-chains 100 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 60 optimal weight: 0.1980 chunk 35 optimal weight: 0.0670 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.149436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.127580 restraints weight = 7146.699| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.46 r_work: 0.3249 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6760 Z= 0.102 Angle : 0.491 6.242 9227 Z= 0.250 Chirality : 0.039 0.142 1028 Planarity : 0.005 0.043 1164 Dihedral : 9.267 105.300 991 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.19 % Allowed : 13.86 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.75 (0.30), residues: 844 helix: 2.04 (0.29), residues: 360 sheet: 1.16 (0.48), residues: 140 loop : -1.56 (0.29), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 184 HIS 0.003 0.001 HIS C 563 PHE 0.008 0.001 PHE C 349 TYR 0.015 0.001 TYR C 259 ARG 0.003 0.000 ARG C 595 Details of bonding type rmsd hydrogen bonds : bond 0.04274 ( 303) hydrogen bonds : angle 3.46003 ( 900) SS BOND : bond 0.00734 ( 1) SS BOND : angle 1.43643 ( 2) covalent geometry : bond 0.00216 ( 6758) covalent geometry : angle 0.49107 ( 9225) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.832 Fit side-chains REVERT: C 35 ARG cc_start: 0.8117 (tpp80) cc_final: 0.7823 (tpp-160) REVERT: C 284 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8044 (mttp) REVERT: C 287 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7314 (mt0) REVERT: C 314 MET cc_start: 0.8115 (ttp) cc_final: 0.7690 (ttt) REVERT: C 336 ILE cc_start: 0.8186 (mp) cc_final: 0.7841 (mm) REVERT: C 398 MET cc_start: 0.6259 (mmt) cc_final: 0.5671 (mtp) REVERT: C 404 TYR cc_start: 0.6387 (m-10) cc_final: 0.6105 (m-10) REVERT: C 444 ASP cc_start: 0.7536 (t70) cc_final: 0.7243 (t70) REVERT: C 479 ASN cc_start: 0.8438 (m-40) cc_final: 0.8108 (m-40) REVERT: C 644 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7628 (tm-30) REVERT: B 43 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8184 (mptp) outliers start: 8 outliers final: 4 residues processed: 86 average time/residue: 1.4078 time to fit residues: 128.4851 Evaluate side-chains 87 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain B residue 43 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 71 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.146302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.124211 restraints weight = 7202.059| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.50 r_work: 0.3197 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6760 Z= 0.132 Angle : 0.543 5.805 9227 Z= 0.278 Chirality : 0.041 0.163 1028 Planarity : 0.006 0.043 1164 Dihedral : 9.335 102.189 991 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.64 % Allowed : 13.86 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.65 (0.30), residues: 844 helix: 1.97 (0.29), residues: 360 sheet: 0.83 (0.47), residues: 147 loop : -1.54 (0.29), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 115 HIS 0.005 0.001 HIS C 563 PHE 0.012 0.001 PHE C 349 TYR 0.016 0.001 TYR C 259 ARG 0.004 0.000 ARG C 595 Details of bonding type rmsd hydrogen bonds : bond 0.05453 ( 303) hydrogen bonds : angle 3.56877 ( 900) SS BOND : bond 0.00998 ( 1) SS BOND : angle 2.00381 ( 2) covalent geometry : bond 0.00303 ( 6758) covalent geometry : angle 0.54272 ( 9225) Misc. bond : bond 0.00054 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.707 Fit side-chains REVERT: C 35 ARG cc_start: 0.8229 (tpp80) cc_final: 0.7938 (tpp-160) REVERT: C 110 ARG cc_start: 0.6371 (mtt90) cc_final: 0.5882 (ttt180) REVERT: C 284 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8152 (mttp) REVERT: C 287 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7465 (mt0) REVERT: C 336 ILE cc_start: 0.8183 (mp) cc_final: 0.7924 (mm) REVERT: C 398 MET cc_start: 0.6493 (mmt) cc_final: 0.5899 (mtp) REVERT: C 404 TYR cc_start: 0.6637 (m-10) cc_final: 0.6395 (m-10) REVERT: C 444 ASP cc_start: 0.7778 (t70) cc_final: 0.7523 (t70) REVERT: C 451 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.6638 (mp10) REVERT: C 479 ASN cc_start: 0.8457 (m-40) cc_final: 0.8109 (m-40) REVERT: C 644 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7684 (tm-30) REVERT: A 11 SER cc_start: 0.8408 (OUTLIER) cc_final: 0.7989 (p) REVERT: B 43 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8236 (mptp) outliers start: 11 outliers final: 5 residues processed: 93 average time/residue: 1.6763 time to fit residues: 163.2671 Evaluate side-chains 96 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.146447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.124124 restraints weight = 7165.077| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.49 r_work: 0.3211 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6760 Z= 0.123 Angle : 0.530 5.651 9227 Z= 0.271 Chirality : 0.041 0.155 1028 Planarity : 0.005 0.043 1164 Dihedral : 9.288 103.544 991 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.94 % Allowed : 13.71 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.65 (0.30), residues: 844 helix: 1.97 (0.29), residues: 360 sheet: 0.82 (0.47), residues: 147 loop : -1.54 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 184 HIS 0.004 0.001 HIS C 563 PHE 0.011 0.001 PHE C 349 TYR 0.016 0.001 TYR C 259 ARG 0.003 0.000 ARG C 494 Details of bonding type rmsd hydrogen bonds : bond 0.05282 ( 303) hydrogen bonds : angle 3.56794 ( 900) SS BOND : bond 0.00940 ( 1) SS BOND : angle 1.83343 ( 2) covalent geometry : bond 0.00276 ( 6758) covalent geometry : angle 0.52981 ( 9225) Misc. bond : bond 0.00046 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6069.21 seconds wall clock time: 107 minutes 13.39 seconds (6433.39 seconds total)