Starting phenix.real_space_refine on Wed Aug 5 02:21:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dtt_47165/08_2026/9dtt_47165.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dtt_47165/08_2026/9dtt_47165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dtt_47165/08_2026/9dtt_47165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dtt_47165/08_2026/9dtt_47165.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dtt_47165/08_2026/9dtt_47165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dtt_47165/08_2026/9dtt_47165.map" } resolution = 3.6 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= 0.001 sd= 0.034 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 Zn 2 6.06 5 P 66 5.49 5 S 47 5.16 5 C 4940 2.51 5 N 1489 2.21 5 O 1730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8274 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 6844 Classifications: {'peptide': 850} Link IDs: {'PTRANS': 31, 'TRANS': 818} Chain breaks: 10 Chain: "B" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1428 Classifications: {'RNA': 67} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 30, 'rna3p_pyr': 26} Link IDs: {'rna2p': 11, 'rna3p': 55} Chain: "A" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3387 SG CYS A 447 38.079 31.174 14.910 1.00 65.84 S ATOM 3409 SG CYS A 450 35.736 32.847 18.002 1.00 59.79 S ATOM 5557 SG CYS A 728 39.612 35.472 62.904 1.00 82.32 S ATOM 6542 SG CYS A 847 42.380 37.452 64.857 1.00 89.41 S Time building chain proxies: 1.42, per 1000 atoms: 0.17 Number of scatterers: 8274 At special positions: 0 Unit cell: (84.724, 102.674, 119.906, 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 2 29.99 S 47 16.00 P 66 15.00 O 1730 8.00 N 1489 7.00 C 4940 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: 0.81 Conformation dependent library (CDL) restraints added in 148.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 450 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 442 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 447 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" NE2 HIS A 714 " pdb="ZN ZN A1002 " - pdb=" NE2 HIS A 712 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 847 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 728 " Number of angles added : 2 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 7 sheets defined 48.7% alpha, 8.9% beta 16 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 10 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 4.012A pdb=" N LYS A 30 " --> pdb=" O GLN A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 48 removed outlier: 3.730A pdb=" N GLU A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.914A pdb=" N LYS A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG A 68 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 93 removed outlier: 3.982A pdb=" N GLY A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.534A pdb=" N THR A 135 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 169 removed outlier: 3.779A pdb=" N GLU A 157 " --> pdb=" O ASN A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 228 through 242 Processing helix chain 'A' and resid 273 through 289 removed outlier: 4.082A pdb=" N ILE A 277 " --> pdb=" O ASN A 273 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LYS A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ARG A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 328 removed outlier: 3.864A pdb=" N LEU A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 335 through 343 removed outlier: 3.540A pdb=" N THR A 339 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 358 Processing helix chain 'A' and resid 367 through 386 Processing helix chain 'A' and resid 395 through 402 removed outlier: 4.099A pdb=" N PHE A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 429 removed outlier: 3.573A pdb=" N ALA A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 427 " --> pdb=" O ARG A 423 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 removed outlier: 4.338A pdb=" N GLU A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 478 through 490 removed outlier: 3.520A pdb=" N LEU A 484 " --> pdb=" O GLY A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 496 removed outlier: 3.647A pdb=" N HIS A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 525 removed outlier: 3.638A pdb=" N SER A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS A 524 " --> pdb=" O ARG A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 removed outlier: 3.811A pdb=" N LEU A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 543 through 548' Processing helix chain 'A' and resid 549 through 556 removed outlier: 3.558A pdb=" N HIS A 556 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 572 Processing helix chain 'A' and resid 605 through 627 removed outlier: 3.603A pdb=" N LEU A 609 " --> pdb=" O GLY A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 657 removed outlier: 6.547A pdb=" N ARG A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLU A 653 " --> pdb=" O ARG A 649 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 684 removed outlier: 3.607A pdb=" N MET A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.735A pdb=" N GLN A 705 " --> pdb=" O ASP A 702 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 706 " --> pdb=" O TRP A 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 702 through 706' Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 748 through 766 Processing helix chain 'A' and resid 770 through 783 Processing helix chain 'A' and resid 801 through 805 removed outlier: 3.790A pdb=" N MET A 804 " --> pdb=" O HIS A 801 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A 805 " --> pdb=" O GLU A 802 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 801 through 805' Processing helix chain 'A' and resid 808 through 818 Processing helix chain 'A' and resid 840 through 847 Processing helix chain 'A' and resid 853 through 862 Processing helix chain 'A' and resid 862 through 875 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 removed outlier: 3.533A pdb=" N GLU A 35 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 126 removed outlier: 6.123A pdb=" N GLY A 75 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 99 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU A 103 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 143 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LYS A 181 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N CYS A 145 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A 180 " --> pdb=" O TRP A 220 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 304 through 311 removed outlier: 6.575A pdb=" N TYR A 305 " --> pdb=" O SER A 594 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER A 594 " --> pdb=" O TYR A 305 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY A 307 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR A 588 " --> pdb=" O THR A 311 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 320 through 321 Processing sheet with id=AA5, first strand: chain 'A' and resid 659 through 661 removed outlier: 4.243A pdb=" N CYS A 665 " --> pdb=" O ASP A 533 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP A 533 " --> pdb=" O CYS A 665 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 535 through 536 removed outlier: 4.235A pdb=" N VAL A 687 " --> pdb=" O ALA A 536 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 712 through 717 281 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2432 1.34 - 1.46: 1812 1.46 - 1.57: 4132 1.57 - 1.69: 132 1.69 - 1.81: 80 Bond restraints: 8588 Sorted by residual: bond pdb=" N9 A B 13 " pdb=" C4 A B 13 " ideal model delta sigma weight residual 1.374 1.381 -0.007 6.00e-03 2.78e+04 1.40e+00 bond pdb=" N9 A B 56 " pdb=" C4 A B 56 " ideal model delta sigma weight residual 1.374 1.381 -0.007 6.00e-03 2.78e+04 1.18e+00 bond pdb=" C8 G B 28 " pdb=" N7 G B 28 " ideal model delta sigma weight residual 1.305 1.299 0.006 6.00e-03 2.78e+04 1.16e+00 bond pdb=" C3' G B 40 " pdb=" O3' G B 40 " ideal model delta sigma weight residual 1.417 1.431 -0.014 1.40e-02 5.10e+03 1.01e+00 bond pdb=" C4 C B 14 " pdb=" C5 C B 14 " ideal model delta sigma weight residual 1.425 1.418 0.007 8.00e-03 1.56e+04 8.22e-01 ... (remaining 8583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 11446 1.34 - 2.68: 403 2.68 - 4.02: 54 4.02 - 5.36: 9 5.36 - 6.71: 3 Bond angle restraints: 11915 Sorted by residual: angle pdb=" N1 C B 14 " pdb=" C6 C B 14 " pdb=" C5 C B 14 " ideal model delta sigma weight residual 121.00 122.94 -1.94 5.00e-01 4.00e+00 1.51e+01 angle pdb=" O5' G B 46 " pdb=" C5' G B 46 " pdb=" C4' G B 46 " ideal model delta sigma weight residual 109.40 112.50 -3.10 8.00e-01 1.56e+00 1.50e+01 angle pdb=" O5' A B 13 " pdb=" C5' A B 13 " pdb=" C4' A B 13 " ideal model delta sigma weight residual 109.40 112.44 -3.04 8.00e-01 1.56e+00 1.45e+01 angle pdb=" C3' G B 40 " pdb=" O3' G B 40 " pdb=" P A B 41 " ideal model delta sigma weight residual 119.70 124.25 -4.55 1.20e+00 6.94e-01 1.44e+01 angle pdb=" O5' C B 20 " pdb=" C5' C B 20 " pdb=" C4' C B 20 " ideal model delta sigma weight residual 109.40 112.24 -2.84 8.00e-01 1.56e+00 1.26e+01 ... (remaining 11910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.03: 4673 23.03 - 46.05: 360 46.05 - 69.08: 137 69.08 - 92.11: 34 92.11 - 115.13: 3 Dihedral angle restraints: 5207 sinusoidal: 2780 harmonic: 2427 Sorted by residual: dihedral pdb=" O4' C B 30 " pdb=" C1' C B 30 " pdb=" N1 C B 30 " pdb=" C2 C B 30 " ideal model delta sinusoidal sigma weight residual -128.00 -65.59 -62.41 1 1.70e+01 3.46e-03 1.78e+01 dihedral pdb=" O4' G B 32 " pdb=" C1' G B 32 " pdb=" N9 G B 32 " pdb=" C4 G B 32 " ideal model delta sinusoidal sigma weight residual -106.00 -156.64 50.64 1 1.70e+01 3.46e-03 1.22e+01 dihedral pdb=" CA TRP A 700 " pdb=" C TRP A 700 " pdb=" N ASN A 701 " pdb=" CA ASN A 701 " ideal model delta harmonic sigma weight residual 180.00 163.08 16.92 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 5204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 875 0.033 - 0.065: 292 0.065 - 0.098: 84 0.098 - 0.130: 40 0.130 - 0.163: 44 Chirality restraints: 1335 Sorted by residual: chirality pdb=" C3' G B 40 " pdb=" C4' G B 40 " pdb=" O3' G B 40 " pdb=" C2' G B 40 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" C2' G B 40 " pdb=" C3' G B 40 " pdb=" O2' G B 40 " pdb=" C1' G B 40 " both_signs ideal model delta sigma weight residual False -2.62 -2.78 0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" CA ILE A 717 " pdb=" N ILE A 717 " pdb=" C ILE A 717 " pdb=" CB ILE A 717 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.20e-01 ... (remaining 1332 not shown) Planarity restraints: 1270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 13 " 0.022 2.00e-02 2.50e+03 1.02e-02 2.89e+00 pdb=" N9 A B 13 " -0.025 2.00e-02 2.50e+03 pdb=" C8 A B 13 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A B 13 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A B 13 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 13 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A B 13 " 0.005 2.00e-02 2.50e+03 pdb=" N1 A B 13 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A B 13 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A B 13 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A B 13 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 220 " 0.010 2.00e-02 2.50e+03 1.02e-02 2.61e+00 pdb=" CG TRP A 220 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 220 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 220 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP A 220 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 220 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 220 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 220 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 220 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 220 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 706 " 0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO A 707 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 707 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 707 " 0.019 5.00e-02 4.00e+02 ... (remaining 1267 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 224 2.69 - 3.24: 7683 3.24 - 3.79: 13272 3.79 - 4.35: 16762 4.35 - 4.90: 26164 Nonbonded interactions: 64105 Sorted by model distance: nonbonded pdb=" O GLY A 602 " pdb=" OG1 THR A 606 " model vdw 2.136 3.040 nonbonded pdb=" ND2 ASN A 273 " pdb=" OD1 ASP A 275 " model vdw 2.187 3.120 nonbonded pdb=" O2' G B 40 " pdb=" OP1 A B 41 " model vdw 2.229 3.040 nonbonded pdb=" O ASN A 610 " pdb=" ND2 ASN A 614 " model vdw 2.277 3.120 nonbonded pdb=" O2' G B 22 " pdb=" OP1 C B 24 " model vdw 2.286 3.040 ... (remaining 64100 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.600 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3962 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8595 Z= 0.122 Angle : 0.570 6.705 11917 Z= 0.391 Chirality : 0.046 0.163 1335 Planarity : 0.003 0.035 1270 Dihedral : 18.762 115.133 3641 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.29), residues: 830 helix: 0.83 (0.29), residues: 355 sheet: -0.63 (0.62), residues: 70 loop : -1.59 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 769 TYR 0.011 0.001 TYR A 452 PHE 0.012 0.001 PHE A 178 TRP 0.024 0.001 TRP A 220 HIS 0.005 0.001 HIS A 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.12 ( 8588) covalent geometry : angle 0.56906 / 0.39 (11915) hydrogen bonds : bond 0.13976 / 9.51 ( 320) hydrogen bonds : angle 6.60387 / 4.75 ( 866) metal coordination : bond 0.00623 / 0.37 ( 7) metal coordination : angle 3.00807 / 1.58 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ARG cc_start: 0.3731 (mpt90) cc_final: 0.1066 (ptp90) REVERT: A 367 LYS cc_start: 0.5634 (mmtm) cc_final: 0.5221 (mmtm) REVERT: A 534 ASP cc_start: 0.7143 (p0) cc_final: 0.6857 (p0) REVERT: A 689 LYS cc_start: 0.7046 (pptt) cc_final: 0.6309 (tptt) REVERT: A 770 ARG cc_start: 0.3436 (mtt90) cc_final: 0.2497 (ptp90) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.0955 time to fit residues: 15.5622 Evaluate side-chains 92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.0470 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 overall best weight: 1.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS A 213 ASN A 581 GLN ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 GLN A 777 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.202615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.191516 restraints weight = 30306.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.193593 restraints weight = 17879.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.195138 restraints weight = 11560.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.196211 restraints weight = 8180.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.196888 restraints weight = 6219.431| |-----------------------------------------------------------------------------| r_work (final): 0.4849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3998 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8595 Z= 0.131 Angle : 0.580 10.654 11917 Z= 0.307 Chirality : 0.040 0.283 1335 Planarity : 0.004 0.034 1270 Dihedral : 18.379 118.644 1942 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.08 % Allowed : 8.12 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.28), residues: 830 helix: 0.54 (0.27), residues: 373 sheet: -0.69 (0.60), residues: 70 loop : -1.89 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 739 TYR 0.014 0.002 TYR A 838 PHE 0.020 0.002 PHE A 483 TRP 0.012 0.001 TRP A 803 HIS 0.009 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 8588) covalent geometry : angle 0.57382 / 0.31 (11915) hydrogen bonds : bond 0.05808 / 4.01 ( 320) hydrogen bonds : angle 5.17223 / 3.56 ( 866) metal coordination : bond 0.01534 / 0.76 ( 7) metal coordination : angle 6.36344 / 3.50 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ARG cc_start: 0.4057 (mpt90) cc_final: 0.1294 (ptp90) REVERT: A 320 MET cc_start: 0.5770 (mpp) cc_final: 0.5563 (mpp) REVERT: A 534 ASP cc_start: 0.7118 (p0) cc_final: 0.6902 (p0) REVERT: A 668 LYS cc_start: 0.6609 (tttm) cc_final: 0.6266 (tttm) REVERT: A 689 LYS cc_start: 0.6922 (pptt) cc_final: 0.6188 (tptm) REVERT: A 770 ARG cc_start: 0.3349 (mtt90) cc_final: 0.1963 (ptp90) REVERT: A 824 MET cc_start: 0.4298 (mmm) cc_final: 0.3026 (mtp) outliers start: 8 outliers final: 1 residues processed: 94 average time/residue: 0.0832 time to fit residues: 10.5921 Evaluate side-chains 86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 90 optimal weight: 40.0000 chunk 38 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 88 optimal weight: 40.0000 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 555 ASN ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** 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 = 0.4892 r_free = 0.4892 target = 0.200306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.189250 restraints weight = 30046.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.191378 restraints weight = 17346.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.192876 restraints weight = 11022.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.193902 restraints weight = 7734.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.194567 restraints weight = 5875.877| |-----------------------------------------------------------------------------| r_work (final): 0.4824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4093 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 8595 Z= 0.147 Angle : 0.595 10.415 11917 Z= 0.315 Chirality : 0.042 0.289 1335 Planarity : 0.004 0.051 1270 Dihedral : 18.466 121.081 1942 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.35 % Allowed : 10.28 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.28), residues: 830 helix: 0.31 (0.27), residues: 374 sheet: -0.71 (0.65), residues: 60 loop : -2.04 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.014 0.002 TYR A 476 PHE 0.022 0.002 PHE A 708 TRP 0.016 0.002 TRP A 303 HIS 0.006 0.002 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 8588) covalent geometry : angle 0.58746 / 0.31 (11915) hydrogen bonds : bond 0.05350 / 3.64 ( 320) hydrogen bonds : angle 5.11297 / 3.49 ( 866) metal coordination : bond 0.01363 / 0.71 ( 7) metal coordination : angle 7.40646 / 3.90 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.0597 (ptt) cc_final: 0.0336 (ptt) REVERT: A 246 ARG cc_start: 0.4263 (mpt90) cc_final: 0.1417 (ptp90) REVERT: A 534 ASP cc_start: 0.7256 (p0) cc_final: 0.7044 (p0) REVERT: A 668 LYS cc_start: 0.6891 (tttm) cc_final: 0.6584 (tttm) REVERT: A 689 LYS cc_start: 0.6954 (pptt) cc_final: 0.6309 (tptt) REVERT: A 770 ARG cc_start: 0.3237 (mtt90) cc_final: 0.1586 (ptp90) REVERT: A 824 MET cc_start: 0.4808 (mmm) cc_final: 0.3618 (mtp) outliers start: 10 outliers final: 5 residues processed: 98 average time/residue: 0.0833 time to fit residues: 11.1681 Evaluate side-chains 88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 813 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN A 364 GLN ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.200902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.190002 restraints weight = 30414.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.192076 restraints weight = 17825.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.193492 restraints weight = 11500.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.194574 restraints weight = 8047.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.195306 restraints weight = 6063.042| |-----------------------------------------------------------------------------| r_work (final): 0.4829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4038 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8595 Z= 0.119 Angle : 0.582 9.261 11917 Z= 0.305 Chirality : 0.039 0.282 1335 Planarity : 0.005 0.080 1270 Dihedral : 18.451 121.524 1942 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.35 % Allowed : 13.53 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.28), residues: 830 helix: 0.34 (0.27), residues: 377 sheet: -0.79 (0.66), residues: 62 loop : -2.06 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 362 TYR 0.010 0.002 TYR A 476 PHE 0.019 0.002 PHE A 708 TRP 0.031 0.001 TRP A 419 HIS 0.004 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 8588) covalent geometry : angle 0.57721 / 0.30 (11915) hydrogen bonds : bond 0.05015 / 3.45 ( 320) hydrogen bonds : angle 4.96853 / 3.36 ( 866) metal coordination : bond 0.00988 / 0.54 ( 7) metal coordination : angle 5.74993 / 3.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 245 MET cc_start: 0.0811 (ptt) cc_final: 0.0540 (ptt) REVERT: A 246 ARG cc_start: 0.4412 (mpt90) cc_final: 0.1541 (ptp90) REVERT: A 367 LYS cc_start: 0.5527 (mmtm) cc_final: 0.3561 (tptp) REVERT: A 534 ASP cc_start: 0.7253 (p0) cc_final: 0.7052 (p0) REVERT: A 689 LYS cc_start: 0.6933 (pptt) cc_final: 0.6291 (tptt) REVERT: A 770 ARG cc_start: 0.3292 (mtt90) cc_final: 0.1979 (ptp90) REVERT: A 824 MET cc_start: 0.4994 (mmm) cc_final: 0.3894 (mtp) outliers start: 10 outliers final: 7 residues processed: 98 average time/residue: 0.0894 time to fit residues: 11.9921 Evaluate side-chains 90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 803 TRP Chi-restraints excluded: chain A residue 813 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 85 optimal weight: 30.0000 chunk 67 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 90 optimal weight: 40.0000 chunk 42 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN A 288 HIS ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.199032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.187832 restraints weight = 30126.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.189911 restraints weight = 17908.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.191338 restraints weight = 11419.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.192445 restraints weight = 7984.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.193122 restraints weight = 6007.700| |-----------------------------------------------------------------------------| r_work (final): 0.4808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4150 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8595 Z= 0.156 Angle : 0.630 9.333 11917 Z= 0.333 Chirality : 0.042 0.285 1335 Planarity : 0.005 0.083 1270 Dihedral : 18.545 122.233 1942 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.89 % Allowed : 14.88 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.28), residues: 830 helix: 0.10 (0.27), residues: 370 sheet: -0.93 (0.66), residues: 62 loop : -2.11 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 212 TYR 0.014 0.002 TYR A 476 PHE 0.020 0.002 PHE A 708 TRP 0.018 0.002 TRP A 803 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 8588) covalent geometry : angle 0.62469 / 0.33 (11915) hydrogen bonds : bond 0.05332 / 3.61 ( 320) hydrogen bonds : angle 5.09474 / 3.45 ( 866) metal coordination : bond 0.00866 / 0.45 ( 7) metal coordination : angle 6.61715 / 3.48 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.4770 (mmm) cc_final: 0.3504 (mtt) REVERT: A 245 MET cc_start: 0.0901 (ptt) cc_final: 0.0625 (ptt) REVERT: A 246 ARG cc_start: 0.4546 (mpt90) cc_final: 0.1618 (ptp90) REVERT: A 367 LYS cc_start: 0.5734 (mmtm) cc_final: 0.3622 (tptp) REVERT: A 423 ARG cc_start: 0.6281 (tpt170) cc_final: 0.6020 (tpt170) REVERT: A 534 ASP cc_start: 0.7321 (p0) cc_final: 0.7117 (p0) REVERT: A 689 LYS cc_start: 0.6943 (pptt) cc_final: 0.6305 (tptt) REVERT: A 770 ARG cc_start: 0.3335 (mtt90) cc_final: 0.2228 (ptp-170) REVERT: A 797 ILE cc_start: 0.4805 (OUTLIER) cc_final: 0.4277 (tp) REVERT: A 824 MET cc_start: 0.5170 (mmm) cc_final: 0.4021 (mtp) outliers start: 14 outliers final: 8 residues processed: 95 average time/residue: 0.0896 time to fit residues: 11.5188 Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 803 TRP Chi-restraints excluded: chain A residue 813 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 68 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 86 optimal weight: 30.0000 chunk 17 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 ASN ** 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 = 0.4881 r_free = 0.4881 target = 0.199226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.188238 restraints weight = 29757.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.190324 restraints weight = 17377.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.191836 restraints weight = 11131.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.192824 restraints weight = 7763.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.193516 restraints weight = 5888.719| |-----------------------------------------------------------------------------| r_work (final): 0.4812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4134 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8595 Z= 0.131 Angle : 0.602 8.817 11917 Z= 0.318 Chirality : 0.041 0.286 1335 Planarity : 0.005 0.070 1270 Dihedral : 18.581 122.493 1942 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.30 % Allowed : 15.83 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.28), residues: 830 helix: 0.02 (0.26), residues: 377 sheet: -0.95 (0.66), residues: 62 loop : -2.14 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 212 TYR 0.015 0.002 TYR A 252 PHE 0.019 0.002 PHE A 708 TRP 0.018 0.001 TRP A 803 HIS 0.004 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 8588) covalent geometry : angle 0.59702 / 0.32 (11915) hydrogen bonds : bond 0.05113 / 3.51 ( 320) hydrogen bonds : angle 5.04003 / 3.41 ( 866) metal coordination : bond 0.01009 / 0.55 ( 7) metal coordination : angle 5.73915 / 3.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.1002 (ptt) cc_final: 0.0722 (ptt) REVERT: A 246 ARG cc_start: 0.4588 (mpt90) cc_final: 0.1618 (ptp90) REVERT: A 367 LYS cc_start: 0.5569 (mmtm) cc_final: 0.3532 (tptp) REVERT: A 689 LYS cc_start: 0.6914 (pptt) cc_final: 0.6288 (tptt) REVERT: A 717 ILE cc_start: 0.3086 (mm) cc_final: 0.2841 (mm) REVERT: A 770 ARG cc_start: 0.3357 (mtt90) cc_final: 0.1845 (ptp90) REVERT: A 824 MET cc_start: 0.5275 (mmm) cc_final: 0.4047 (mtp) outliers start: 17 outliers final: 9 residues processed: 97 average time/residue: 0.0983 time to fit residues: 12.8373 Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 813 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 83 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 75 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.200434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.189500 restraints weight = 30324.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.191622 restraints weight = 17446.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.193024 restraints weight = 11087.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.194098 restraints weight = 7822.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.194771 restraints weight = 5855.191| |-----------------------------------------------------------------------------| r_work (final): 0.4828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4063 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8595 Z= 0.105 Angle : 0.586 9.473 11917 Z= 0.305 Chirality : 0.039 0.288 1335 Planarity : 0.004 0.058 1270 Dihedral : 18.516 122.249 1942 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.30 % Allowed : 15.29 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.28), residues: 830 helix: 0.15 (0.27), residues: 377 sheet: -0.87 (0.68), residues: 62 loop : -2.08 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 212 TYR 0.009 0.001 TYR A 476 PHE 0.020 0.002 PHE A 708 TRP 0.025 0.001 TRP A 803 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 8588) covalent geometry : angle 0.58284 / 0.30 (11915) hydrogen bonds : bond 0.04786 / 3.31 ( 320) hydrogen bonds : angle 4.90385 / 3.31 ( 866) metal coordination : bond 0.01199 / 0.68 ( 7) metal coordination : angle 4.34572 / 2.29 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.4743 (mmm) cc_final: 0.3464 (mtt) REVERT: A 245 MET cc_start: 0.0942 (ptt) cc_final: 0.0639 (ptt) REVERT: A 246 ARG cc_start: 0.4578 (mpt90) cc_final: 0.1598 (ptp90) REVERT: A 367 LYS cc_start: 0.5408 (mmtm) cc_final: 0.3547 (tptp) REVERT: A 423 ARG cc_start: 0.6322 (tpt170) cc_final: 0.6099 (tpt170) REVERT: A 689 LYS cc_start: 0.6869 (pptt) cc_final: 0.6294 (tptt) REVERT: A 770 ARG cc_start: 0.3267 (mtt90) cc_final: 0.1983 (ptp90) REVERT: A 824 MET cc_start: 0.5185 (mmm) cc_final: 0.3924 (mtp) outliers start: 17 outliers final: 12 residues processed: 96 average time/residue: 0.0962 time to fit residues: 12.4948 Evaluate side-chains 93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 803 TRP Chi-restraints excluded: chain A residue 813 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 6 optimal weight: 0.0870 chunk 75 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 42 optimal weight: 6.9990 chunk 10 optimal weight: 0.3980 chunk 80 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 chunk 55 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN A 705 GLN ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.201649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.190922 restraints weight = 29954.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.192996 restraints weight = 17952.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.194454 restraints weight = 11529.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.195501 restraints weight = 8045.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.196182 restraints weight = 6067.326| |-----------------------------------------------------------------------------| r_work (final): 0.4839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3990 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8595 Z= 0.103 Angle : 0.580 9.180 11917 Z= 0.303 Chirality : 0.040 0.290 1335 Planarity : 0.004 0.051 1270 Dihedral : 18.440 121.878 1942 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.76 % Allowed : 15.56 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.28), residues: 830 helix: 0.25 (0.27), residues: 378 sheet: -0.71 (0.67), residues: 62 loop : -2.13 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 599 TYR 0.010 0.001 TYR A 607 PHE 0.058 0.002 PHE A 708 TRP 0.019 0.001 TRP A 803 HIS 0.005 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 8588) covalent geometry : angle 0.57820 / 0.30 (11915) hydrogen bonds : bond 0.04606 / 3.19 ( 320) hydrogen bonds : angle 4.82598 / 3.24 ( 866) metal coordination : bond 0.01329 / 0.76 ( 7) metal coordination : angle 3.74606 / 1.97 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.1738 (tpt) cc_final: -0.0293 (ptt) REVERT: A 245 MET cc_start: 0.0984 (ptt) cc_final: 0.0633 (ptt) REVERT: A 246 ARG cc_start: 0.4643 (mpt90) cc_final: 0.1681 (ptp90) REVERT: A 367 LYS cc_start: 0.5217 (mmtm) cc_final: 0.3554 (tptp) REVERT: A 423 ARG cc_start: 0.6275 (tpt170) cc_final: 0.6067 (tpt170) REVERT: A 689 LYS cc_start: 0.6866 (pptt) cc_final: 0.6318 (tptt) REVERT: A 770 ARG cc_start: 0.3238 (mtt90) cc_final: 0.1791 (ptp90) REVERT: A 824 MET cc_start: 0.5044 (mmm) cc_final: 0.3895 (mtp) outliers start: 13 outliers final: 12 residues processed: 94 average time/residue: 0.0876 time to fit residues: 11.2688 Evaluate side-chains 93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 803 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 42 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 64 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 25 optimal weight: 0.0570 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN ** A 712 HIS ** 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 = 0.4902 r_free = 0.4902 target = 0.201802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.191270 restraints weight = 30331.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.193358 restraints weight = 17827.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.194660 restraints weight = 11336.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.195714 restraints weight = 7924.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.196342 restraints weight = 5973.793| |-----------------------------------------------------------------------------| r_work (final): 0.4845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4044 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8595 Z= 0.103 Angle : 0.583 10.083 11917 Z= 0.303 Chirality : 0.039 0.291 1335 Planarity : 0.004 0.045 1270 Dihedral : 18.380 121.629 1942 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.62 % Allowed : 16.91 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.28), residues: 830 helix: 0.33 (0.27), residues: 378 sheet: -0.99 (0.61), residues: 72 loop : -2.08 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 599 TYR 0.009 0.001 TYR A 607 PHE 0.030 0.002 PHE A 708 TRP 0.027 0.001 TRP A 803 HIS 0.006 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 8588) covalent geometry : angle 0.58162 / 0.30 (11915) hydrogen bonds : bond 0.04456 / 3.09 ( 320) hydrogen bonds : angle 4.77830 / 3.21 ( 866) metal coordination : bond 0.01249 / 0.72 ( 7) metal coordination : angle 3.61974 / 1.91 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 238 MET cc_start: 0.1506 (tpt) cc_final: -0.0414 (ptt) REVERT: A 245 MET cc_start: 0.0725 (ptt) cc_final: 0.0327 (ptt) REVERT: A 246 ARG cc_start: 0.4446 (mpt90) cc_final: 0.1495 (ptp90) REVERT: A 367 LYS cc_start: 0.5435 (mmtm) cc_final: 0.3576 (tptp) REVERT: A 423 ARG cc_start: 0.6371 (tpt170) cc_final: 0.6165 (tpt170) REVERT: A 689 LYS cc_start: 0.6918 (pptt) cc_final: 0.6286 (tptt) REVERT: A 770 ARG cc_start: 0.3165 (mtt90) cc_final: 0.1904 (ptp90) REVERT: A 824 MET cc_start: 0.5195 (mmm) cc_final: 0.4038 (mtp) outliers start: 12 outliers final: 9 residues processed: 90 average time/residue: 0.0931 time to fit residues: 11.1776 Evaluate side-chains 85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 772 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN ** A 712 HIS ** 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 = 0.4883 r_free = 0.4883 target = 0.200092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.189691 restraints weight = 30050.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.191736 restraints weight = 17791.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.193027 restraints weight = 11366.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.194055 restraints weight = 7929.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.194665 restraints weight = 5959.594| |-----------------------------------------------------------------------------| r_work (final): 0.4826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4109 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8595 Z= 0.134 Angle : 0.629 10.502 11917 Z= 0.327 Chirality : 0.041 0.289 1335 Planarity : 0.004 0.045 1270 Dihedral : 18.385 121.857 1942 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.22 % Allowed : 16.91 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.28), residues: 830 helix: 0.19 (0.27), residues: 380 sheet: -1.15 (0.59), residues: 72 loop : -2.14 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 773 TYR 0.011 0.002 TYR A 186 PHE 0.014 0.002 PHE A 708 TRP 0.036 0.002 TRP A 813 HIS 0.006 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 8588) covalent geometry : angle 0.62621 / 0.33 (11915) hydrogen bonds : bond 0.04723 / 3.25 ( 320) hydrogen bonds : angle 4.83673 / 3.24 ( 866) metal coordination : bond 0.00858 / 0.47 ( 7) metal coordination : angle 4.58531 / 2.42 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 238 MET cc_start: 0.1567 (tpt) cc_final: -0.0460 (ptt) REVERT: A 245 MET cc_start: 0.0842 (ptt) cc_final: 0.0521 (ptt) REVERT: A 246 ARG cc_start: 0.4622 (mpt90) cc_final: 0.1594 (ptp90) REVERT: A 367 LYS cc_start: 0.5564 (mmtm) cc_final: 0.3581 (tptp) REVERT: A 423 ARG cc_start: 0.6365 (tpt170) cc_final: 0.6160 (tpt170) REVERT: A 599 ARG cc_start: 0.6137 (mmm-85) cc_final: 0.5515 (tpp80) REVERT: A 689 LYS cc_start: 0.6916 (pptt) cc_final: 0.6334 (tptt) REVERT: A 770 ARG cc_start: 0.3339 (mtt90) cc_final: 0.1919 (ptp90) REVERT: A 824 MET cc_start: 0.5227 (mmm) cc_final: 0.3934 (mtp) outliers start: 9 outliers final: 8 residues processed: 83 average time/residue: 0.0822 time to fit residues: 9.2539 Evaluate side-chains 82 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 772 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 63 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 88 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN ** A 712 HIS ** 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 = 0.4885 r_free = 0.4885 target = 0.200063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.189251 restraints weight = 30409.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.191382 restraints weight = 17818.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.192792 restraints weight = 11376.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.193858 restraints weight = 7914.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.194529 restraints weight = 5935.847| |-----------------------------------------------------------------------------| r_work (final): 0.4824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4093 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8595 Z= 0.129 Angle : 0.617 10.445 11917 Z= 0.322 Chirality : 0.041 0.288 1335 Planarity : 0.005 0.050 1270 Dihedral : 18.375 121.978 1942 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.08 % Allowed : 16.78 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.28), residues: 830 helix: 0.18 (0.27), residues: 381 sheet: -1.18 (0.59), residues: 72 loop : -2.16 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 657 TYR 0.011 0.002 TYR A 186 PHE 0.012 0.002 PHE A 708 TRP 0.034 0.002 TRP A 813 HIS 0.006 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8588) covalent geometry : angle 0.61431 / 0.32 (11915) hydrogen bonds : bond 0.04739 / 3.27 ( 320) hydrogen bonds : angle 4.83582 / 3.24 ( 866) metal coordination : bond 0.00890 / 0.49 ( 7) metal coordination : angle 4.36431 / 2.30 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1423.64 seconds wall clock time: 25 minutes 12.55 seconds (1512.55 seconds total)