Starting phenix.real_space_refine on Wed Sep 17 07:13:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dlf_46976/09_2025/9dlf_46976_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dlf_46976/09_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_46976/09_2025/9dlf_46976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dlf_46976/09_2025/9dlf_46976.map" model { file = "/net/cci-nas-00/data/ceres_data/9dlf_46976/09_2025/9dlf_46976_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dlf_46976/09_2025/9dlf_46976_neut.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.063 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.81, per 1000 atoms: 0.28 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: 0.58 Conformation dependent library (CDL) restraints added in 397.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.26 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: 1.02 Time building geometry restraints manager: 0.78 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: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.360 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.380 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG C 494 TYR 0.040 0.002 TYR B 100 PHE 0.025 0.002 PHE C 49 TRP 0.020 0.001 TRP C 33 HIS 0.006 0.001 HIS C 563 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 6758) covalent geometry : angle 0.64907 ( 9225) SS BOND : bond 0.00844 ( 1) SS BOND : angle 1.57840 ( 2) hydrogen bonds : bond 0.18537 ( 303) hydrogen bonds : angle 6.64933 ( 900) 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 : 0.282 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: 0.5789 time to fit residues: 65.7776 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 : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.144662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.122615 restraints weight = 7161.297| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.45 r_work: 0.3163 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6760 Z= 0.163 Angle : 0.615 6.605 9227 Z= 0.318 Chirality : 0.043 0.156 1028 Planarity : 0.006 0.054 1164 Dihedral : 12.818 168.937 991 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.83 % Allowed : 6.41 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.29), residues: 844 helix: 1.35 (0.28), residues: 356 sheet: 0.60 (0.47), residues: 145 loop : -1.61 (0.29), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 35 TYR 0.017 0.002 TYR C 259 PHE 0.013 0.001 PHE C 349 TRP 0.020 0.001 TRP C 33 HIS 0.007 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 6758) covalent geometry : angle 0.61415 ( 9225) SS BOND : bond 0.01277 ( 1) SS BOND : angle 2.28692 ( 2) hydrogen bonds : bond 0.06860 ( 303) hydrogen bonds : angle 4.34799 ( 900) Misc. bond : bond 0.00161 ( 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 100 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.297 Fit side-chains REVERT: C 287 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7418 (mt0) REVERT: C 398 MET cc_start: 0.6419 (mmt) cc_final: 0.5725 (mtp) REVERT: C 478 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: C 479 ASN cc_start: 0.8604 (m-40) cc_final: 0.8191 (m-40) REVERT: C 644 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: B 28 ASN cc_start: 0.9152 (m-40) cc_final: 0.8939 (m110) REVERT: B 90 ASP cc_start: 0.8170 (m-30) cc_final: 0.7901 (m-30) outliers start: 19 outliers final: 9 residues processed: 90 average time/residue: 0.5655 time to fit residues: 53.4199 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 : 0.237 ------------------------------------------------------------------------------- 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 27 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 32 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 53 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.148207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.126286 restraints weight = 7041.060| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.42 r_work: 0.3236 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1277 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 : 0.517 5.946 9227 Z= 0.266 Chirality : 0.040 0.144 1028 Planarity : 0.005 0.043 1164 Dihedral : 11.285 134.283 991 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.24 % Allowed : 8.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.29), residues: 844 helix: 1.75 (0.29), residues: 355 sheet: 0.75 (0.47), residues: 144 loop : -1.60 (0.29), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 146 TYR 0.016 0.001 TYR C 259 PHE 0.009 0.001 PHE C 349 TRP 0.017 0.001 TRP C 33 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6758) covalent geometry : angle 0.51640 ( 9225) SS BOND : bond 0.00932 ( 1) SS BOND : angle 1.66552 ( 2) hydrogen bonds : bond 0.05056 ( 303) hydrogen bonds : angle 3.90544 ( 900) Misc. bond : bond 0.00088 ( 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 97 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.277 Fit side-chains REVERT: C 146 ARG cc_start: 0.7475 (mmt-90) cc_final: 0.7243 (mmt-90) REVERT: C 287 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7296 (mt0) REVERT: C 314 MET cc_start: 0.8049 (ttp) cc_final: 0.7693 (ttt) REVERT: C 317 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6260 (mp) REVERT: C 336 ILE cc_start: 0.8173 (mp) cc_final: 0.7901 (mm) REVERT: C 369 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.7046 (mtt) REVERT: C 398 MET cc_start: 0.6297 (mmt) cc_final: 0.5640 (mtp) REVERT: C 404 TYR cc_start: 0.6611 (m-10) cc_final: 0.6399 (m-10) REVERT: C 444 ASP cc_start: 0.7651 (t70) cc_final: 0.7367 (t70) REVERT: C 479 ASN cc_start: 0.8515 (m-40) cc_final: 0.8161 (m-40) REVERT: C 644 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: B 28 ASN cc_start: 0.9078 (m-40) cc_final: 0.8872 (m110) REVERT: B 90 ASP cc_start: 0.8129 (m-30) cc_final: 0.7884 (m-30) outliers start: 15 outliers final: 8 residues processed: 93 average time/residue: 0.5694 time to fit residues: 55.7664 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 : 0.253 ------------------------------------------------------------------------------- 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 369 MET 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 61 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 81 optimal weight: 0.0670 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.147908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.125843 restraints weight = 7170.022| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.49 r_work: 0.3224 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6760 Z= 0.114 Angle : 0.519 6.236 9227 Z= 0.266 Chirality : 0.040 0.144 1028 Planarity : 0.006 0.043 1164 Dihedral : 10.402 106.263 991 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.13 % Allowed : 8.64 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.30), residues: 844 helix: 1.88 (0.29), residues: 360 sheet: 0.81 (0.47), residues: 144 loop : -1.59 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 145 TYR 0.016 0.001 TYR C 259 PHE 0.011 0.001 PHE C 349 TRP 0.009 0.001 TRP C 33 HIS 0.008 0.001 HIS C 563 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 6758) covalent geometry : angle 0.51813 ( 9225) SS BOND : bond 0.00917 ( 1) SS BOND : angle 1.63274 ( 2) hydrogen bonds : bond 0.04992 ( 303) hydrogen bonds : angle 3.69749 ( 900) Misc. bond : bond 0.00060 ( 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 99 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.243 Fit side-chains REVERT: C 146 ARG cc_start: 0.7423 (mmt-90) cc_final: 0.7168 (mmt-90) REVERT: C 287 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7363 (mt0) REVERT: C 336 ILE cc_start: 0.8245 (mp) cc_final: 0.7974 (mm) REVERT: C 398 MET cc_start: 0.6235 (mmt) cc_final: 0.5689 (mtm) REVERT: C 404 TYR cc_start: 0.6574 (m-10) cc_final: 0.6304 (m-10) REVERT: C 444 ASP cc_start: 0.7702 (t70) cc_final: 0.7431 (t70) REVERT: C 479 ASN cc_start: 0.8500 (m-40) cc_final: 0.8156 (m-40) REVERT: C 644 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: A 90 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7819 (tp40) REVERT: B 90 ASP cc_start: 0.8171 (m-30) cc_final: 0.7939 (m-30) outliers start: 21 outliers final: 14 residues processed: 92 average time/residue: 0.5742 time to fit residues: 55.6167 Evaluate side-chains 93 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 241 THR 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 369 MET 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 606 THR 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 A residue 104 LYS Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 0.0970 chunk 70 optimal weight: 0.7980 chunk 67 optimal weight: 0.0970 chunk 19 optimal weight: 0.0970 chunk 51 optimal weight: 4.9990 overall best weight: 0.6176 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.148594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.126530 restraints weight = 7202.594| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.49 r_work: 0.3173 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1470 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= 0.110 Angle : 0.510 6.093 9227 Z= 0.260 Chirality : 0.040 0.150 1028 Planarity : 0.005 0.044 1164 Dihedral : 9.920 101.409 991 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.53 % Allowed : 10.13 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.30), residues: 844 helix: 1.95 (0.29), residues: 360 sheet: 0.80 (0.47), residues: 146 loop : -1.54 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 145 TYR 0.016 0.001 TYR C 259 PHE 0.010 0.001 PHE C 349 TRP 0.008 0.001 TRP C 184 HIS 0.002 0.000 HIS C 563 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 6758) covalent geometry : angle 0.50964 ( 9225) SS BOND : bond 0.00899 ( 1) SS BOND : angle 1.69791 ( 2) hydrogen bonds : bond 0.04804 ( 303) hydrogen bonds : angle 3.57815 ( 900) Misc. bond : bond 0.00052 ( 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 100 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.200 Fit side-chains REVERT: C 110 ARG cc_start: 0.6390 (mtt90) cc_final: 0.5873 (ttt180) REVERT: C 146 ARG cc_start: 0.7611 (mmt-90) cc_final: 0.7350 (mmt-90) REVERT: C 284 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8110 (mttp) REVERT: C 287 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7379 (mt0) REVERT: C 317 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.6252 (mp) REVERT: C 336 ILE cc_start: 0.8295 (mp) cc_final: 0.8029 (mm) REVERT: C 398 MET cc_start: 0.6388 (mmt) cc_final: 0.5705 (mtm) REVERT: C 404 TYR cc_start: 0.6584 (m-10) cc_final: 0.6282 (m-10) REVERT: C 451 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6903 (mp10) REVERT: C 479 ASN cc_start: 0.8528 (m-40) cc_final: 0.8197 (m-40) REVERT: C 644 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: B 90 ASP cc_start: 0.8242 (m-30) cc_final: 0.8004 (m-30) outliers start: 17 outliers final: 9 residues processed: 93 average time/residue: 0.5832 time to fit residues: 57.1140 Evaluate side-chains 93 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 451 GLN Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 644 GLU Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain B residue 12 VAL 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 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 27 optimal weight: 0.0870 chunk 54 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.148733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.126718 restraints weight = 7168.365| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.49 r_work: 0.3235 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1549 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= 0.109 Angle : 0.505 5.983 9227 Z= 0.257 Chirality : 0.040 0.152 1028 Planarity : 0.005 0.044 1164 Dihedral : 9.558 101.801 991 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.83 % Allowed : 10.88 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.30), residues: 844 helix: 2.00 (0.29), residues: 360 sheet: 0.73 (0.47), residues: 147 loop : -1.47 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 595 TYR 0.016 0.001 TYR C 259 PHE 0.010 0.001 PHE C 349 TRP 0.008 0.001 TRP C 184 HIS 0.008 0.001 HIS C 563 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 6758) covalent geometry : angle 0.50491 ( 9225) SS BOND : bond 0.00872 ( 1) SS BOND : angle 1.66582 ( 2) hydrogen bonds : bond 0.04713 ( 303) hydrogen bonds : angle 3.50722 ( 900) Misc. bond : bond 0.00048 ( 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 99 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.265 Fit side-chains REVERT: C 110 ARG cc_start: 0.6326 (mtt90) cc_final: 0.5839 (ttt180) REVERT: C 146 ARG cc_start: 0.7505 (mmt-90) cc_final: 0.7267 (mmt-90) REVERT: C 284 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8080 (mttp) REVERT: C 287 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7357 (mt0) REVERT: C 317 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6258 (mp) REVERT: C 336 ILE cc_start: 0.8182 (mp) cc_final: 0.7913 (mm) REVERT: C 398 MET cc_start: 0.6383 (mmt) cc_final: 0.5710 (mtm) REVERT: C 404 TYR cc_start: 0.6449 (m-10) cc_final: 0.6157 (m-10) REVERT: C 444 ASP cc_start: 0.7657 (t70) cc_final: 0.7362 (t70) REVERT: C 451 GLN cc_start: 0.7438 (mp10) cc_final: 0.6739 (mp10) REVERT: C 479 ASN cc_start: 0.8452 (m-40) cc_final: 0.8119 (m-40) REVERT: C 644 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: A 45 LYS cc_start: 0.8213 (mptt) cc_final: 0.7510 (mmtm) REVERT: A 90 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7947 (tp40) REVERT: B 90 ASP cc_start: 0.8169 (m-30) cc_final: 0.7934 (m-30) outliers start: 19 outliers final: 12 residues processed: 93 average time/residue: 0.5709 time to fit residues: 56.0052 Evaluate side-chains 96 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 606 THR 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 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 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 77 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 0.0010 chunk 33 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.150601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.128322 restraints weight = 7081.629| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.52 r_work: 0.3256 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1663 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= 0.098 Angle : 0.483 6.120 9227 Z= 0.244 Chirality : 0.039 0.143 1028 Planarity : 0.005 0.044 1164 Dihedral : 9.248 103.802 991 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.83 % Allowed : 11.77 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.30), residues: 844 helix: 2.12 (0.29), residues: 360 sheet: 0.81 (0.47), residues: 146 loop : -1.45 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 595 TYR 0.015 0.001 TYR C 259 PHE 0.009 0.001 PHE C 349 TRP 0.007 0.001 TRP C 184 HIS 0.002 0.000 HIS C 563 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 6758) covalent geometry : angle 0.48221 ( 9225) SS BOND : bond 0.00758 ( 1) SS BOND : angle 1.47205 ( 2) hydrogen bonds : bond 0.04127 ( 303) hydrogen bonds : angle 3.39627 ( 900) Misc. bond : bond 0.00035 ( 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 104 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.260 Fit side-chains REVERT: C 35 ARG cc_start: 0.8120 (tpp80) cc_final: 0.7737 (tpp-160) REVERT: C 110 ARG cc_start: 0.6309 (mtt90) cc_final: 0.5799 (ttt180) REVERT: C 284 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8091 (mttp) REVERT: C 287 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7394 (mt0) REVERT: C 317 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6276 (mp) REVERT: C 336 ILE cc_start: 0.8160 (mp) cc_final: 0.7909 (mm) REVERT: C 398 MET cc_start: 0.6338 (mmt) cc_final: 0.5686 (mtm) REVERT: C 479 ASN cc_start: 0.8465 (m-40) cc_final: 0.8139 (m-40) REVERT: C 644 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7684 (tm-30) REVERT: A 77 SER cc_start: 0.7276 (OUTLIER) cc_final: 0.6793 (t) REVERT: A 90 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7966 (tp40) REVERT: B 90 ASP cc_start: 0.8199 (m-30) cc_final: 0.7986 (m-30) outliers start: 19 outliers final: 10 residues processed: 99 average time/residue: 0.5889 time to fit residues: 61.3962 Evaluate side-chains 98 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 317 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 540 ILE 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 A residue 77 SER Chi-restraints excluded: chain A residue 90 GLN 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 78 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 54 optimal weight: 0.3980 chunk 67 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.148256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.126026 restraints weight = 7064.623| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.43 r_work: 0.3223 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6760 Z= 0.118 Angle : 0.524 5.757 9227 Z= 0.266 Chirality : 0.040 0.154 1028 Planarity : 0.005 0.043 1164 Dihedral : 9.283 101.426 991 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.83 % Allowed : 11.92 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.30), residues: 844 helix: 2.04 (0.29), residues: 360 sheet: 0.76 (0.47), residues: 147 loop : -1.50 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 146 TYR 0.016 0.001 TYR C 259 PHE 0.012 0.001 PHE C 349 TRP 0.009 0.001 TRP C 33 HIS 0.006 0.001 HIS C 563 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6758) covalent geometry : angle 0.52322 ( 9225) SS BOND : bond 0.00933 ( 1) SS BOND : angle 1.82769 ( 2) hydrogen bonds : bond 0.05021 ( 303) hydrogen bonds : angle 3.48257 ( 900) Misc. bond : bond 0.00050 ( 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 101 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.266 Fit side-chains REVERT: C 35 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7874 (tpp-160) REVERT: C 110 ARG cc_start: 0.6307 (mtt90) cc_final: 0.5801 (ttt180) REVERT: C 284 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8140 (mttp) REVERT: C 287 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7460 (mt0) REVERT: C 314 MET cc_start: 0.8241 (ttp) cc_final: 0.7818 (ttt) REVERT: C 317 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6311 (mp) REVERT: C 336 ILE cc_start: 0.8224 (mp) cc_final: 0.7972 (mm) REVERT: C 398 MET cc_start: 0.6471 (mmt) cc_final: 0.5830 (mtp) REVERT: C 404 TYR cc_start: 0.6535 (m-10) cc_final: 0.6264 (m-10) REVERT: C 451 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.6782 (mp10) REVERT: C 479 ASN cc_start: 0.8446 (m-40) cc_final: 0.8108 (m-40) REVERT: C 644 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: A 77 SER cc_start: 0.7353 (OUTLIER) cc_final: 0.6897 (t) REVERT: A 90 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8026 (tp40) outliers start: 19 outliers final: 9 residues processed: 96 average time/residue: 0.5696 time to fit residues: 57.4589 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 : 0.244 ------------------------------------------------------------------------------- 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 317 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 405 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 A residue 77 SER Chi-restraints excluded: chain A residue 90 GLN 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 24 optimal weight: 0.0000 chunk 17 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.149036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.126767 restraints weight = 7092.148| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.44 r_work: 0.3233 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1666 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= 0.110 Angle : 0.507 5.791 9227 Z= 0.258 Chirality : 0.040 0.150 1028 Planarity : 0.005 0.043 1164 Dihedral : 9.201 103.516 991 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.30), residues: 844 helix: 2.06 (0.29), residues: 361 sheet: 0.78 (0.47), residues: 147 loop : -1.47 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 146 TYR 0.016 0.001 TYR C 259 PHE 0.010 0.001 PHE C 349 TRP 0.008 0.001 TRP C 33 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 6758) covalent geometry : angle 0.50683 ( 9225) SS BOND : bond 0.00862 ( 1) SS BOND : angle 1.67889 ( 2) hydrogen bonds : bond 0.04722 ( 303) hydrogen bonds : angle 3.44295 ( 900) Misc. bond : bond 0.00043 ( 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 98 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.294 Fit side-chains REVERT: C 35 ARG cc_start: 0.8174 (tpp80) cc_final: 0.7881 (tpp-160) REVERT: C 110 ARG cc_start: 0.6314 (mtt90) cc_final: 0.5806 (ttt180) REVERT: C 284 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8168 (mttp) REVERT: C 287 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7472 (mt0) REVERT: C 317 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6355 (mp) REVERT: C 336 ILE cc_start: 0.8213 (mp) cc_final: 0.7971 (mm) REVERT: C 398 MET cc_start: 0.6486 (mmt) cc_final: 0.5850 (mtp) REVERT: C 451 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.6799 (mp10) REVERT: C 479 ASN cc_start: 0.8450 (m-40) cc_final: 0.8114 (m-40) REVERT: C 644 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: A 11 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.7927 (p) REVERT: A 77 SER cc_start: 0.7295 (OUTLIER) cc_final: 0.6856 (t) REVERT: A 90 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8031 (tp40) outliers start: 16 outliers final: 7 residues processed: 95 average time/residue: 0.6500 time to fit residues: 64.7217 Evaluate side-chains 97 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 317 LEU Chi-restraints excluded: chain C residue 405 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 A residue 77 SER Chi-restraints excluded: chain A residue 90 GLN 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 50 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 563 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.146558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.124148 restraints weight = 7094.979| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.57 r_work: 0.3205 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1632 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= 0.128 Angle : 0.542 5.844 9227 Z= 0.276 Chirality : 0.041 0.158 1028 Planarity : 0.006 0.044 1164 Dihedral : 9.276 102.466 991 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 : 2.53 % Allowed : 12.82 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.30), residues: 844 helix: 1.96 (0.28), residues: 361 sheet: 0.78 (0.47), residues: 147 loop : -1.51 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 146 TYR 0.016 0.001 TYR C 259 PHE 0.011 0.001 PHE C 349 TRP 0.009 0.001 TRP B 115 HIS 0.005 0.001 HIS C 563 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6758) covalent geometry : angle 0.54120 ( 9225) SS BOND : bond 0.00996 ( 1) SS BOND : angle 1.94121 ( 2) hydrogen bonds : bond 0.05423 ( 303) hydrogen bonds : angle 3.52225 ( 900) Misc. bond : bond 0.00050 ( 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 102 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.261 Fit side-chains REVERT: C 35 ARG cc_start: 0.8208 (tpp80) cc_final: 0.7929 (tpp-160) REVERT: C 110 ARG cc_start: 0.6350 (mtt90) cc_final: 0.5847 (ttt180) REVERT: C 284 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8107 (mttp) REVERT: C 287 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7423 (mt0) REVERT: C 317 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6355 (mp) REVERT: C 336 ILE cc_start: 0.8271 (mp) cc_final: 0.8014 (mm) REVERT: C 398 MET cc_start: 0.6405 (mmt) cc_final: 0.5793 (mtp) REVERT: C 404 TYR cc_start: 0.6542 (m-10) cc_final: 0.6325 (m-10) REVERT: C 451 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6753 (mp10) REVERT: C 479 ASN cc_start: 0.8474 (m-40) cc_final: 0.8124 (m-40) REVERT: C 644 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: A 11 SER cc_start: 0.8406 (OUTLIER) cc_final: 0.7985 (p) REVERT: A 77 SER cc_start: 0.7317 (OUTLIER) cc_final: 0.6918 (t) outliers start: 17 outliers final: 8 residues processed: 96 average time/residue: 0.6309 time to fit residues: 63.5207 Evaluate side-chains 99 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 317 LEU Chi-restraints excluded: chain C residue 405 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 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 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 61 optimal weight: 0.3980 chunk 68 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 72 optimal weight: 0.0020 chunk 70 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.150316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.128151 restraints weight = 7092.871| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.50 r_work: 0.3260 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1795 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= 0.099 Angle : 0.488 5.944 9227 Z= 0.247 Chirality : 0.039 0.147 1028 Planarity : 0.005 0.045 1164 Dihedral : 9.002 105.848 991 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.24 % Allowed : 13.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.30), residues: 844 helix: 2.14 (0.29), residues: 361 sheet: 0.92 (0.47), residues: 146 loop : -1.49 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 595 TYR 0.015 0.001 TYR C 259 PHE 0.008 0.001 PHE C 349 TRP 0.008 0.001 TRP C 184 HIS 0.004 0.001 HIS C 563 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 6758) covalent geometry : angle 0.48738 ( 9225) SS BOND : bond 0.00717 ( 1) SS BOND : angle 1.39568 ( 2) hydrogen bonds : bond 0.04104 ( 303) hydrogen bonds : angle 3.36837 ( 900) Misc. bond : bond 0.00028 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2472.59 seconds wall clock time: 42 minutes 53.29 seconds (2573.29 seconds total)