Starting phenix.real_space_refine on Fri Nov 15 06:32:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpc_16149/11_2024/8bpc_16149_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpc_16149/11_2024/8bpc_16149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpc_16149/11_2024/8bpc_16149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpc_16149/11_2024/8bpc_16149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpc_16149/11_2024/8bpc_16149_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpc_16149/11_2024/8bpc_16149_neut.cif" } resolution = 2.8 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 3 6.06 5 S 55 5.16 5 C 5342 2.51 5 N 1449 2.21 5 O 1582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8433 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4405 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 17, 'TRANS': 518} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 368, 2956 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 351} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 113} Chain breaks: 1 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 22 Unusual residues: {' CA': 2, ' ZN': 1, 'SHH': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7745 SG CYS C 289 37.812 59.778 45.110 1.00 57.24 S ATOM 7771 SG CYS C 292 35.245 58.180 42.684 1.00 45.08 S ATOM 7954 SG CYS C 315 38.906 57.170 42.432 1.00 59.56 S ATOM 7629 SG CYS C 274 38.038 47.655 47.545 1.00 38.25 S ATOM 7653 SG CYS C 277 37.502 44.027 48.618 1.00 48.40 S ATOM 7837 SG CYS C 300 41.011 45.328 48.053 1.00 41.17 S Time building chain proxies: 5.25, per 1000 atoms: 0.62 Number of scatterers: 8433 At special positions: 0 Unit cell: (121.92, 93.472, 110.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 Ca 2 19.99 S 55 16.00 O 1582 8.00 N 1449 7.00 C 5342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 995.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" ND1 HIS B 179 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 318 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 292 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 315 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 289 " pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" ND1 HIS C 297 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 300 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 277 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 274 " Number of angles added : 6 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1950 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 59.5% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.861A pdb=" N PHE A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 336 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 417 through 424 Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.548A pdb=" N LYS A 445 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 484 removed outlier: 3.647A pdb=" N LEU A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 removed outlier: 4.222A pdb=" N GLU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 519 through 530 Processing helix chain 'A' and resid 530 through 561 Proline residue: A 536 - end of helix Processing helix chain 'A' and resid 563 through 573 removed outlier: 5.035A pdb=" N LEU A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LYS A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 587 removed outlier: 4.095A pdb=" N GLN A 581 " --> pdb=" O VAL A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 610 removed outlier: 3.556A pdb=" N ILE A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 643 removed outlier: 3.626A pdb=" N LEU A 630 " --> pdb=" O ASP A 626 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG A 643 " --> pdb=" O TYR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 661 through 667 Processing helix chain 'A' and resid 746 through 786 removed outlier: 3.651A pdb=" N LEU A 786 " --> pdb=" O GLU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 792 Processing helix chain 'A' and resid 808 through 829 removed outlier: 5.040A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Proline residue: A 817 - end of helix Processing helix chain 'A' and resid 832 through 845 Processing helix chain 'A' and resid 846 through 852 removed outlier: 4.708A pdb=" N TYR A 849 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 850 " --> pdb=" O HIS A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 871 Processing helix chain 'A' and resid 871 through 887 removed outlier: 3.530A pdb=" N LEU A 875 " --> pdb=" O ASP A 871 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 887 " --> pdb=" O ASN A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 915 removed outlier: 5.412A pdb=" N ALA A 902 " --> pdb=" O CYS A 898 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ARG A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.726A pdb=" N TYR B 23 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 46 removed outlier: 3.923A pdb=" N ARG B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 70 through 80 Processing helix chain 'B' and resid 81 through 87 removed outlier: 4.114A pdb=" N MET B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N SER B 86 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU B 87 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'B' and resid 106 through 127 removed outlier: 3.703A pdb=" N SER B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.582A pdb=" N LEU B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 234 through 254 removed outlier: 3.618A pdb=" N LYS B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Proline residue: B 244 - end of helix Processing helix chain 'B' and resid 278 through 292 removed outlier: 4.069A pdb=" N CYS B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL B 286 " --> pdb=" O HIS B 282 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 321 Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.648A pdb=" N GLY B 339 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 372 Processing helix chain 'C' and resid 20 through 28 Processing helix chain 'C' and resid 319 through 324 removed outlier: 3.714A pdb=" N VAL C 323 " --> pdb=" O ILE C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 340 removed outlier: 3.616A pdb=" N ARG C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 397 removed outlier: 3.718A pdb=" N ILE A 397 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 620 through 624 removed outlier: 4.314A pdb=" N VAL A 739 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 55 removed outlier: 6.618A pdb=" N CYS B 13 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 133 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B 258 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LEU B 299 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B 260 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 172 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N GLN B 261 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE B 174 " --> pdb=" O GLN B 261 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL B 171 " --> pdb=" O MET B 195 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL B 197 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR B 173 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N PHE B 199 " --> pdb=" O TYR B 173 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP B 175 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N LYS B 201 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N VAL B 225 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N THR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N PHE B 227 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER B 198 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N MET B 229 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N HIS B 200 " --> pdb=" O MET B 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 286 through 288 428 hydrogen bonds defined for protein. 1239 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: 2.47 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2156 1.33 - 1.46: 1852 1.46 - 1.58: 4484 1.58 - 1.70: 0 1.70 - 1.83: 82 Bond restraints: 8574 Sorted by residual: bond pdb=" CA SER A 430 " pdb=" CB SER A 430 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.34e-02 5.57e+03 1.08e+01 bond pdb=" N THR A 446 " pdb=" CA THR A 446 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.14e-02 7.69e+03 8.99e+00 bond pdb=" N TRP A 434 " pdb=" CA TRP A 434 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.16e-02 7.43e+03 8.80e+00 bond pdb=" N VAL A 429 " pdb=" CA VAL A 429 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.19e-02 7.06e+03 7.82e+00 bond pdb=" N LYS B 11 " pdb=" CA LYS B 11 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.21e-02 6.83e+03 7.44e+00 ... (remaining 8569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 11317 2.13 - 4.26: 214 4.26 - 6.39: 31 6.39 - 8.52: 3 8.52 - 10.65: 2 Bond angle restraints: 11567 Sorted by residual: angle pdb=" O PRO C 30 " pdb=" C PRO C 30 " pdb=" N PRO C 31 " ideal model delta sigma weight residual 121.31 117.73 3.58 4.60e-01 4.73e+00 6.06e+01 angle pdb=" C THR A 427 " pdb=" N TRP A 428 " pdb=" CA TRP A 428 " ideal model delta sigma weight residual 122.64 112.99 9.65 1.70e+00 3.46e-01 3.22e+01 angle pdb=" N PRO C 31 " pdb=" CA PRO C 31 " pdb=" CB PRO C 31 " ideal model delta sigma weight residual 102.35 105.94 -3.59 7.10e-01 1.98e+00 2.56e+01 angle pdb=" C VAL A 429 " pdb=" N SER A 430 " pdb=" CA SER A 430 " ideal model delta sigma weight residual 122.77 116.84 5.93 1.33e+00 5.65e-01 1.99e+01 angle pdb=" C GLU A 789 " pdb=" CA GLU A 789 " pdb=" CB GLU A 789 " ideal model delta sigma weight residual 116.63 111.48 5.15 1.16e+00 7.43e-01 1.97e+01 ... (remaining 11562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4429 17.83 - 35.66: 528 35.66 - 53.49: 185 53.49 - 71.31: 30 71.31 - 89.14: 11 Dihedral angle restraints: 5183 sinusoidal: 2159 harmonic: 3024 Sorted by residual: dihedral pdb=" CA THR B 305 " pdb=" C THR B 305 " pdb=" N ILE B 306 " pdb=" CA ILE B 306 " ideal model delta harmonic sigma weight residual -180.00 -157.68 -22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA GLU A 562 " pdb=" C GLU A 562 " pdb=" N GLN A 563 " pdb=" CA GLN A 563 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA TYR B 304 " pdb=" C TYR B 304 " pdb=" N THR B 305 " pdb=" CA THR B 305 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1116 0.071 - 0.142: 110 0.142 - 0.213: 5 0.213 - 0.284: 1 0.284 - 0.355: 2 Chirality restraints: 1234 Sorted by residual: chirality pdb=" CB VAL B 12 " pdb=" CA VAL B 12 " pdb=" CG1 VAL B 12 " pdb=" CG2 VAL B 12 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CB VAL A 441 " pdb=" CA VAL A 441 " pdb=" CG1 VAL A 441 " pdb=" CG2 VAL A 441 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB VAL A 429 " pdb=" CA VAL A 429 " pdb=" CG1 VAL A 429 " pdb=" CG2 VAL A 429 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1231 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 SHH B 501 " 0.008 2.00e-02 2.50e+03 1.91e-02 6.40e+00 pdb=" C11 SHH B 501 " -0.012 2.00e-02 2.50e+03 pdb=" C12 SHH B 501 " -0.007 2.00e-02 2.50e+03 pdb=" C13 SHH B 501 " 0.001 2.00e-02 2.50e+03 pdb=" C14 SHH B 501 " -0.004 2.00e-02 2.50e+03 pdb=" C9 SHH B 501 " 0.040 2.00e-02 2.50e+03 pdb=" N2 SHH B 501 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 269 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO C 270 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 270 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 270 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C7 SHH B 501 " -0.015 2.00e-02 2.50e+03 1.57e-02 3.09e+00 pdb=" C8 SHH B 501 " 0.008 2.00e-02 2.50e+03 pdb=" C9 SHH B 501 " -0.019 2.00e-02 2.50e+03 pdb=" N2 SHH B 501 " 0.024 2.00e-02 2.50e+03 pdb=" O3 SHH B 501 " 0.001 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 12 2.23 - 2.89: 3249 2.89 - 3.56: 11985 3.56 - 4.23: 19656 4.23 - 4.90: 34082 Nonbonded interactions: 68984 Sorted by model distance: nonbonded pdb=" O HOH B 608 " pdb=" O HOH B 632 " model vdw 1.557 3.040 nonbonded pdb=" OH TYR B 16 " pdb=" O HOH B 601 " model vdw 1.648 3.040 nonbonded pdb=" OE2 GLU A 461 " pdb=" O HOH A1201 " model vdw 1.815 3.040 nonbonded pdb=" OD2 ASP B 265 " pdb="ZN ZN B 502 " model vdw 1.919 2.230 nonbonded pdb=" OD1 ASP B 177 " pdb="ZN ZN B 502 " model vdw 1.946 2.230 ... (remaining 68979 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.650 Find NCS groups from input model: 0.090 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:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8574 Z= 0.268 Angle : 0.686 10.650 11567 Z= 0.411 Chirality : 0.045 0.355 1234 Planarity : 0.004 0.047 1500 Dihedral : 17.594 89.143 3233 Min Nonbonded Distance : 1.557 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.18 % Allowed : 24.34 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 0.55 (0.27), residues: 1016 helix: 1.13 (0.23), residues: 551 sheet: 0.60 (0.62), residues: 76 loop : -0.73 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 434 HIS 0.007 0.001 HIS A 867 PHE 0.012 0.001 PHE A 744 TYR 0.014 0.001 TYR B 304 ARG 0.004 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5659 (mp) REVERT: A 395 LYS cc_start: 0.3960 (mttt) cc_final: 0.3599 (ttpt) REVERT: A 486 MET cc_start: 0.6555 (ptt) cc_final: 0.6302 (ptp) REVERT: C 21 MET cc_start: 0.8165 (tpp) cc_final: 0.7847 (tpt) outliers start: 29 outliers final: 5 residues processed: 210 average time/residue: 1.3798 time to fit residues: 305.9016 Evaluate side-chains 106 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 319 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 ASN A 773 GLN A 919 ASN B 22 ASN B 58 HIS B 96 ASN B 226 ASN C 288 GLN C 328 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8574 Z= 0.333 Angle : 0.652 12.316 11567 Z= 0.339 Chirality : 0.045 0.193 1234 Planarity : 0.005 0.049 1500 Dihedral : 5.195 50.741 1148 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 6.47 % Allowed : 20.29 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 0.67 (0.26), residues: 1016 helix: 1.30 (0.22), residues: 559 sheet: 0.77 (0.63), residues: 74 loop : -0.87 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 560 HIS 0.010 0.002 HIS A 867 PHE 0.017 0.002 PHE A 662 TYR 0.020 0.002 TYR B 304 ARG 0.022 0.001 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 109 time to evaluate : 0.986 Fit side-chains REVERT: A 328 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5711 (mp) REVERT: A 342 SER cc_start: 0.3102 (OUTLIER) cc_final: 0.2618 (m) REVERT: A 395 LYS cc_start: 0.4553 (mttt) cc_final: 0.3957 (ttmt) REVERT: A 476 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8707 (mp) REVERT: A 486 MET cc_start: 0.6727 (ptt) cc_final: 0.6314 (ptp) REVERT: A 813 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.7092 (pt0) REVERT: A 875 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7079 (mt) REVERT: B 44 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8518 (mp) REVERT: B 128 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8010 (mt0) REVERT: C 21 MET cc_start: 0.8175 (tpp) cc_final: 0.7929 (tpt) outliers start: 59 outliers final: 15 residues processed: 152 average time/residue: 1.4564 time to fit residues: 234.3234 Evaluate side-chains 98 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 369 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 76 optimal weight: 0.0470 chunk 62 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 ASN A 582 ASN A 603 HIS B 58 HIS C 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8574 Z= 0.163 Angle : 0.507 7.410 11567 Z= 0.269 Chirality : 0.039 0.174 1234 Planarity : 0.004 0.039 1500 Dihedral : 4.867 54.295 1146 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.06 % Allowed : 22.81 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.27), residues: 1016 helix: 1.74 (0.22), residues: 555 sheet: 0.79 (0.63), residues: 76 loop : -0.65 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 434 HIS 0.005 0.001 HIS C 348 PHE 0.014 0.001 PHE A 662 TYR 0.022 0.001 TYR A 740 ARG 0.007 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 1.157 Fit side-chains REVERT: A 328 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5712 (mp) REVERT: A 342 SER cc_start: 0.2677 (OUTLIER) cc_final: 0.2249 (m) REVERT: A 347 LEU cc_start: 0.6491 (mt) cc_final: 0.6223 (tt) REVERT: A 486 MET cc_start: 0.6560 (ptt) cc_final: 0.6244 (ptp) REVERT: A 530 ASN cc_start: 0.7651 (p0) cc_final: 0.7413 (p0) REVERT: C 21 MET cc_start: 0.8167 (tpp) cc_final: 0.7888 (tpt) outliers start: 37 outliers final: 11 residues processed: 113 average time/residue: 1.1794 time to fit residues: 142.9984 Evaluate side-chains 94 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 0.0370 chunk 81 optimal weight: 0.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 603 HIS B 40 HIS B 58 HIS ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8574 Z= 0.171 Angle : 0.493 6.360 11567 Z= 0.259 Chirality : 0.039 0.163 1234 Planarity : 0.004 0.046 1500 Dihedral : 4.788 58.404 1146 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.85 % Allowed : 24.45 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.27), residues: 1016 helix: 1.86 (0.22), residues: 561 sheet: 0.80 (0.64), residues: 76 loop : -0.68 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 434 HIS 0.008 0.001 HIS C 318 PHE 0.015 0.001 PHE A 662 TYR 0.016 0.001 TYR B 304 ARG 0.011 0.000 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.976 Fit side-chains REVERT: A 328 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5673 (mp) REVERT: A 342 SER cc_start: 0.2527 (OUTLIER) cc_final: 0.2158 (m) REVERT: A 347 LEU cc_start: 0.6467 (mt) cc_final: 0.6217 (tt) REVERT: A 486 MET cc_start: 0.6835 (ptt) cc_final: 0.6535 (ptp) REVERT: A 842 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7803 (tm-30) REVERT: C 21 MET cc_start: 0.8196 (tpp) cc_final: 0.7920 (tpt) REVERT: C 272 LYS cc_start: 0.7886 (ptpp) cc_final: 0.7398 (mtpp) outliers start: 26 outliers final: 14 residues processed: 107 average time/residue: 1.1147 time to fit residues: 128.4685 Evaluate side-chains 93 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN A 756 HIS B 58 HIS ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8574 Z= 0.164 Angle : 0.485 6.273 11567 Z= 0.254 Chirality : 0.039 0.153 1234 Planarity : 0.003 0.031 1500 Dihedral : 4.728 57.834 1146 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.52 % Allowed : 25.22 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.27), residues: 1016 helix: 1.94 (0.22), residues: 562 sheet: 0.44 (0.63), residues: 80 loop : -0.60 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 313 HIS 0.005 0.001 HIS C 348 PHE 0.016 0.001 PHE A 662 TYR 0.020 0.001 TYR A 740 ARG 0.009 0.000 ARG A 863 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.929 Fit side-chains REVERT: A 328 LEU cc_start: 0.5902 (OUTLIER) cc_final: 0.5572 (mp) REVERT: A 342 SER cc_start: 0.2450 (OUTLIER) cc_final: 0.2084 (m) REVERT: A 486 MET cc_start: 0.6860 (ptt) cc_final: 0.6570 (ptp) REVERT: A 530 ASN cc_start: 0.7635 (p0) cc_final: 0.7424 (p0) REVERT: A 910 LYS cc_start: 0.6630 (mtpt) cc_final: 0.6223 (tptt) REVERT: C 272 LYS cc_start: 0.7913 (ptpp) cc_final: 0.7431 (mtpp) outliers start: 23 outliers final: 15 residues processed: 98 average time/residue: 1.0786 time to fit residues: 114.2402 Evaluate side-chains 94 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 24 optimal weight: 0.0470 chunk 97 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 58 HIS B 128 GLN ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8574 Z= 0.172 Angle : 0.485 6.471 11567 Z= 0.253 Chirality : 0.039 0.148 1234 Planarity : 0.003 0.031 1500 Dihedral : 4.664 52.985 1146 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.51 % Allowed : 24.34 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.27), residues: 1016 helix: 1.96 (0.22), residues: 563 sheet: 0.42 (0.63), residues: 80 loop : -0.53 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 313 HIS 0.005 0.001 HIS C 348 PHE 0.012 0.001 PHE A 662 TYR 0.016 0.001 TYR B 304 ARG 0.003 0.000 ARG A 900 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 1.044 Fit side-chains REVERT: A 328 LEU cc_start: 0.5835 (OUTLIER) cc_final: 0.5576 (mm) REVERT: A 342 SER cc_start: 0.2519 (OUTLIER) cc_final: 0.2119 (m) REVERT: A 486 MET cc_start: 0.6828 (ptt) cc_final: 0.6489 (ptp) REVERT: A 910 LYS cc_start: 0.6634 (mtpt) cc_final: 0.6387 (tptt) REVERT: C 272 LYS cc_start: 0.7970 (ptpp) cc_final: 0.7579 (mtpp) outliers start: 32 outliers final: 16 residues processed: 104 average time/residue: 1.1883 time to fit residues: 132.6873 Evaluate side-chains 87 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 58 HIS B 93 GLN B 128 GLN ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8574 Z= 0.189 Angle : 0.493 6.568 11567 Z= 0.257 Chirality : 0.039 0.147 1234 Planarity : 0.003 0.033 1500 Dihedral : 4.667 48.653 1146 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.63 % Allowed : 25.00 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.27), residues: 1016 helix: 1.93 (0.22), residues: 563 sheet: 0.40 (0.63), residues: 80 loop : -0.52 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 909 HIS 0.004 0.001 HIS C 348 PHE 0.015 0.001 PHE A 662 TYR 0.017 0.001 TYR B 304 ARG 0.004 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 328 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5678 (mm) REVERT: A 342 SER cc_start: 0.2532 (OUTLIER) cc_final: 0.2143 (m) REVERT: A 486 MET cc_start: 0.6710 (ptt) cc_final: 0.6331 (ptp) REVERT: A 910 LYS cc_start: 0.6567 (mtpt) cc_final: 0.6353 (tptt) REVERT: C 272 LYS cc_start: 0.7802 (ptpp) cc_final: 0.7484 (mtpp) outliers start: 24 outliers final: 16 residues processed: 97 average time/residue: 1.1780 time to fit residues: 123.6495 Evaluate side-chains 91 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 58 HIS B 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8574 Z= 0.172 Angle : 0.481 6.423 11567 Z= 0.252 Chirality : 0.039 0.144 1234 Planarity : 0.003 0.038 1500 Dihedral : 4.626 42.305 1146 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.85 % Allowed : 25.00 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.27), residues: 1016 helix: 1.97 (0.22), residues: 563 sheet: 0.39 (0.63), residues: 80 loop : -0.55 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 749 HIS 0.004 0.001 HIS C 348 PHE 0.010 0.001 PHE A 662 TYR 0.016 0.001 TYR B 304 ARG 0.004 0.000 ARG B 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 342 SER cc_start: 0.2265 (OUTLIER) cc_final: 0.1914 (m) REVERT: A 486 MET cc_start: 0.6679 (ptt) cc_final: 0.6290 (ptp) REVERT: C 272 LYS cc_start: 0.7792 (ptpp) cc_final: 0.7514 (mtpp) REVERT: C 288 GLN cc_start: 0.8100 (tp-100) cc_final: 0.7316 (tm130) outliers start: 26 outliers final: 17 residues processed: 101 average time/residue: 1.1309 time to fit residues: 123.0988 Evaluate side-chains 93 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.0000 chunk 85 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 58 HIS B 93 GLN B 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8574 Z= 0.151 Angle : 0.475 6.383 11567 Z= 0.248 Chirality : 0.038 0.146 1234 Planarity : 0.003 0.039 1500 Dihedral : 4.264 39.581 1144 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.41 % Allowed : 25.11 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.27), residues: 1016 helix: 2.03 (0.22), residues: 563 sheet: 0.36 (0.63), residues: 80 loop : -0.54 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 313 HIS 0.003 0.001 HIS C 348 PHE 0.013 0.001 PHE A 662 TYR 0.021 0.001 TYR A 740 ARG 0.003 0.000 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 342 SER cc_start: 0.2282 (OUTLIER) cc_final: 0.1923 (m) REVERT: A 486 MET cc_start: 0.6629 (ptt) cc_final: 0.6247 (ptp) REVERT: C 272 LYS cc_start: 0.7786 (ptpp) cc_final: 0.7535 (mtpp) outliers start: 22 outliers final: 17 residues processed: 98 average time/residue: 1.1136 time to fit residues: 117.6946 Evaluate side-chains 93 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 chunk 100 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN B 58 HIS B 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8574 Z= 0.246 Angle : 0.540 7.121 11567 Z= 0.282 Chirality : 0.040 0.158 1234 Planarity : 0.004 0.037 1500 Dihedral : 4.691 48.839 1144 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.52 % Allowed : 25.00 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.27), residues: 1016 helix: 1.88 (0.22), residues: 563 sheet: 0.34 (0.58), residues: 84 loop : -0.61 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 749 HIS 0.004 0.001 HIS B 345 PHE 0.015 0.001 PHE A 662 TYR 0.018 0.001 TYR B 304 ARG 0.007 0.000 ARG B 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 1.035 Fit side-chains REVERT: A 342 SER cc_start: 0.2112 (OUTLIER) cc_final: 0.1811 (m) REVERT: A 486 MET cc_start: 0.6592 (ptt) cc_final: 0.6160 (ptp) REVERT: C 272 LYS cc_start: 0.7885 (ptpp) cc_final: 0.7556 (mtpp) REVERT: C 288 GLN cc_start: 0.8194 (tp-100) cc_final: 0.7760 (tm130) REVERT: C 320 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6027 (mm-30) outliers start: 23 outliers final: 15 residues processed: 99 average time/residue: 1.2243 time to fit residues: 130.1699 Evaluate side-chains 91 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 82 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 58 HIS B 93 GLN B 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.164584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118802 restraints weight = 10869.377| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.89 r_work: 0.3292 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8574 Z= 0.167 Angle : 0.485 6.577 11567 Z= 0.254 Chirality : 0.039 0.149 1234 Planarity : 0.003 0.037 1500 Dihedral : 4.548 54.011 1144 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.63 % Allowed : 24.78 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.27), residues: 1016 helix: 1.96 (0.22), residues: 563 sheet: 0.29 (0.60), residues: 85 loop : -0.57 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 313 HIS 0.003 0.001 HIS C 348 PHE 0.010 0.001 PHE A 662 TYR 0.026 0.001 TYR A 740 ARG 0.003 0.000 ARG A 900 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3330.99 seconds wall clock time: 60 minutes 38.62 seconds (3638.62 seconds total)