Starting phenix.real_space_refine on Wed Sep 17 10:52:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dtt_47165/09_2025/9dtt_47165.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dtt_47165/09_2025/9dtt_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_47165/09_2025/9dtt_47165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dtt_47165/09_2025/9dtt_47165.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dtt_47165/09_2025/9dtt_47165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dtt_47165/09_2025/9dtt_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.15, per 1000 atoms: 0.26 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: 0.88 Conformation dependent library (CDL) restraints added in 298.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.05 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: 1.38 Time building geometry restraints manager: 1.12 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=" C3' G B 40 " pdb=" O3' G B 40 " ideal model delta sigma weight residual 1.417 1.431 -0.014 1.50e-02 4.44e+03 8.78e-01 bond pdb=" CE2 PHE A 178 " pdb=" CZ PHE A 178 " ideal model delta sigma weight residual 1.382 1.359 0.023 3.00e-02 1.11e+03 5.95e-01 bond pdb=" CA ARG A 404 " pdb=" C ARG A 404 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.34e-02 5.57e+03 4.48e-01 bond pdb=" C ASN A 227 " pdb=" N ILE A 228 " ideal model delta sigma weight residual 1.338 1.332 0.006 1.01e-02 9.80e+03 3.66e-01 bond pdb=" O3' U B 12 " pdb=" P A B 13 " ideal model delta sigma weight residual 1.607 1.616 -0.009 1.50e-02 4.44e+03 3.64e-01 ... (remaining 8583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 11632 1.34 - 2.68: 231 2.68 - 4.02: 40 4.02 - 5.36: 9 5.36 - 6.71: 3 Bond angle restraints: 11915 Sorted by residual: angle pdb=" O3' G B 40 " pdb=" C3' G B 40 " pdb=" C2' G B 40 " ideal model delta sigma weight residual 113.70 118.03 -4.33 1.50e+00 4.44e-01 8.32e+00 angle pdb=" C3' G B 40 " pdb=" O3' G B 40 " pdb=" P A B 41 " ideal model delta sigma weight residual 120.20 124.25 -4.05 1.50e+00 4.44e-01 7.28e+00 angle pdb=" C GLU A 357 " pdb=" N LYS A 358 " pdb=" CA LYS A 358 " ideal model delta sigma weight residual 122.15 115.66 6.49 2.83e+00 1.25e-01 5.26e+00 angle pdb=" C ASP A 597 " pdb=" N GLN A 598 " pdb=" CA GLN A 598 " ideal model delta sigma weight residual 121.54 125.82 -4.28 1.91e+00 2.74e-01 5.01e+00 angle pdb=" C ARG A 404 " pdb=" N SER A 405 " pdb=" CA SER A 405 " ideal model delta sigma weight residual 121.54 125.67 -4.13 1.91e+00 2.74e-01 4.67e+00 ... (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: 947 0.033 - 0.065: 288 0.065 - 0.098: 73 0.098 - 0.130: 23 0.130 - 0.163: 4 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=" 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 chirality pdb=" CA ILE A 691 " pdb=" N ILE A 691 " pdb=" C ILE A 691 " pdb=" CB ILE A 691 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-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: 2.440 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.110 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3964 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= 0.096 Angle : 0.488 6.705 11917 Z= 0.259 Chirality : 0.036 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 aren 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 covalent geometry : bond 0.00189 ( 8588) covalent geometry : angle 0.48642 (11915) hydrogen bonds : bond 0.13976 ( 320) hydrogen bonds : angle 6.60387 ( 866) metal coordination : bond 0.00623 ( 7) metal coordination : angle 3.00807 ( 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 : 0.273 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: 0.2081 (ptp90) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1248 time to fit residues: 20.0380 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 : 0.291 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 213 ASN A 581 GLN ** 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 = 0.4906 r_free = 0.4906 target = 0.202002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.190856 restraints weight = 30228.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.193048 restraints weight = 17479.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.194661 restraints weight = 11192.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.195741 restraints weight = 7809.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.196424 restraints weight = 5893.517| |-----------------------------------------------------------------------------| r_work (final): 0.4838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3993 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8595 Z= 0.117 Angle : 0.571 9.872 11917 Z= 0.291 Chirality : 0.038 0.219 1335 Planarity : 0.004 0.041 1270 Dihedral : 18.379 115.283 1942 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.08 % Allowed : 7.85 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.29), residues: 830 helix: 0.60 (0.28), residues: 376 sheet: -0.72 (0.60), residues: 72 loop : -1.85 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 739 TYR 0.013 0.002 TYR A 476 PHE 0.014 0.002 PHE A 431 TRP 0.011 0.001 TRP A 220 HIS 0.006 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8588) covalent geometry : angle 0.56299 (11915) hydrogen bonds : bond 0.04547 ( 320) hydrogen bonds : angle 4.97152 ( 866) metal coordination : bond 0.01337 ( 7) metal coordination : angle 7.22107 ( 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 106 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.0571 (ptt) cc_final: 0.0308 (ptt) REVERT: A 246 ARG cc_start: 0.4279 (mpt90) cc_final: 0.1460 (ptp90) REVERT: A 534 ASP cc_start: 0.7179 (p0) cc_final: 0.6938 (p0) REVERT: A 668 LYS cc_start: 0.6559 (tttm) cc_final: 0.6220 (tttm) REVERT: A 689 LYS cc_start: 0.6952 (pptt) cc_final: 0.6311 (tptt) REVERT: A 770 ARG cc_start: 0.3336 (mtt90) cc_final: 0.1948 (ptp-170) REVERT: A 824 MET cc_start: 0.4533 (mmm) cc_final: 0.3862 (mmm) outliers start: 8 outliers final: 2 residues processed: 101 average time/residue: 0.1152 time to fit residues: 15.5192 Evaluate side-chains 90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL 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: 20.0000 chunk 38 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN A 555 ASN ** 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 = 0.4854 r_free = 0.4854 target = 0.196781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.185709 restraints weight = 29819.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.187900 restraints weight = 16985.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.189481 restraints weight = 10740.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.190470 restraints weight = 7381.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.191135 restraints weight = 5527.934| |-----------------------------------------------------------------------------| r_work (final): 0.4789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4249 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 8595 Z= 0.188 Angle : 0.709 11.091 11917 Z= 0.367 Chirality : 0.043 0.220 1335 Planarity : 0.005 0.058 1270 Dihedral : 18.790 118.107 1942 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.84 % Allowed : 11.23 % Favored : 85.93 % 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 aren not related in a simple way. whole: -1.68 (0.27), residues: 830 helix: -0.05 (0.27), residues: 368 sheet: -1.13 (0.62), residues: 64 loop : -2.18 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 749 TYR 0.018 0.002 TYR A 476 PHE 0.022 0.002 PHE A 674 TRP 0.021 0.002 TRP A 497 HIS 0.009 0.002 HIS A 556 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8588) covalent geometry : angle 0.70179 (11915) hydrogen bonds : bond 0.05538 ( 320) hydrogen bonds : angle 5.39159 ( 866) metal coordination : bond 0.01241 ( 7) metal coordination : angle 7.94794 ( 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 111 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ARG cc_start: 0.4635 (mpt90) cc_final: 0.1540 (ttp80) REVERT: A 689 LYS cc_start: 0.7031 (pptt) cc_final: 0.6361 (tptt) REVERT: A 770 ARG cc_start: 0.3439 (mtt90) cc_final: 0.2444 (ptp-170) REVERT: A 824 MET cc_start: 0.4788 (mmm) cc_final: 0.3631 (mtp) outliers start: 21 outliers final: 11 residues processed: 104 average time/residue: 0.1168 time to fit residues: 16.1378 Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 252 TYR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 772 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: 9.9990 chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 40 optimal weight: 0.0060 chunk 66 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4853 r_free = 0.4853 target = 0.196936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.185742 restraints weight = 30258.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.187844 restraints weight = 17332.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.189437 restraints weight = 10984.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.190462 restraints weight = 7594.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.191157 restraints weight = 5676.578| |-----------------------------------------------------------------------------| r_work (final): 0.4789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4240 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 8595 Z= 0.156 Angle : 0.657 9.686 11917 Z= 0.339 Chirality : 0.040 0.222 1335 Planarity : 0.005 0.062 1270 Dihedral : 18.804 118.176 1942 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.71 % Allowed : 13.40 % Favored : 83.90 % 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 aren not related in a simple way. whole: -1.68 (0.28), residues: 830 helix: -0.12 (0.27), residues: 370 sheet: -1.02 (0.64), residues: 64 loop : -2.13 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 749 TYR 0.016 0.002 TYR A 476 PHE 0.017 0.002 PHE A 674 TRP 0.017 0.002 TRP A 497 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8588) covalent geometry : angle 0.65059 (11915) hydrogen bonds : bond 0.05150 ( 320) hydrogen bonds : angle 5.16897 ( 866) metal coordination : bond 0.01129 ( 7) metal coordination : angle 6.91421 ( 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 108 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.1053 (ptt) cc_final: 0.0809 (ptt) REVERT: A 246 ARG cc_start: 0.4731 (mpt90) cc_final: 0.1533 (ttp80) REVERT: A 689 LYS cc_start: 0.6915 (pptt) cc_final: 0.6362 (tptt) REVERT: A 802 GLU cc_start: 0.5202 (tp30) cc_final: 0.4968 (tp30) REVERT: A 824 MET cc_start: 0.5088 (mmm) cc_final: 0.3896 (mtp) REVERT: A 867 ILE cc_start: 0.2554 (OUTLIER) cc_final: 0.2275 (mt) outliers start: 20 outliers final: 9 residues processed: 102 average time/residue: 0.1202 time to fit residues: 16.1392 Evaluate side-chains 91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE 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 483 PHE Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 867 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 37 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 42 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 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 = 0.4870 r_free = 0.4870 target = 0.198253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.187240 restraints weight = 29870.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.189323 restraints weight = 17373.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.190870 restraints weight = 11120.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.191921 restraints weight = 7687.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.192597 restraints weight = 5737.310| |-----------------------------------------------------------------------------| r_work (final): 0.4808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4165 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8595 Z= 0.120 Angle : 0.593 7.840 11917 Z= 0.304 Chirality : 0.038 0.222 1335 Planarity : 0.004 0.051 1270 Dihedral : 18.692 116.948 1942 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.03 % Allowed : 15.83 % 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 aren not related in a simple way. whole: -1.55 (0.28), residues: 830 helix: -0.06 (0.27), residues: 372 sheet: -0.45 (0.68), residues: 62 loop : -2.11 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 621 TYR 0.012 0.001 TYR A 476 PHE 0.014 0.002 PHE A 674 TRP 0.026 0.001 TRP A 803 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8588) covalent geometry : angle 0.58846 (11915) hydrogen bonds : bond 0.04601 ( 320) hydrogen bonds : angle 4.93505 ( 866) metal coordination : bond 0.01213 ( 7) metal coordination : angle 5.56853 ( 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 105 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.4672 (mmm) cc_final: 0.3704 (mtt) REVERT: A 238 MET cc_start: 0.1991 (tpt) cc_final: -0.0207 (ptt) REVERT: A 245 MET cc_start: 0.1049 (ptt) cc_final: 0.0520 (ptp) REVERT: A 246 ARG cc_start: 0.4765 (mpt90) cc_final: 0.1590 (ttp80) REVERT: A 367 LYS cc_start: 0.5709 (mmtm) cc_final: 0.3385 (tptp) REVERT: A 477 MET cc_start: 0.6467 (pmm) cc_final: 0.6203 (pmm) REVERT: A 689 LYS cc_start: 0.6941 (pptt) cc_final: 0.6397 (tptt) REVERT: A 770 ARG cc_start: 0.3447 (mtt90) cc_final: 0.2359 (ptp-170) REVERT: A 824 MET cc_start: 0.4978 (mmm) cc_final: 0.3898 (mtp) outliers start: 15 outliers final: 9 residues processed: 102 average time/residue: 0.1190 time to fit residues: 15.9852 Evaluate side-chains 91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 772 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 68 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 29 optimal weight: 0.0670 chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 30.0000 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN ** 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 = 0.4889 r_free = 0.4889 target = 0.200776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.190195 restraints weight = 29453.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.192249 restraints weight = 17610.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.193584 restraints weight = 11283.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.194658 restraints weight = 7937.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.195344 restraints weight = 5940.240| |-----------------------------------------------------------------------------| r_work (final): 0.4826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4009 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8595 Z= 0.101 Angle : 0.556 7.589 11917 Z= 0.287 Chirality : 0.037 0.219 1335 Planarity : 0.004 0.050 1270 Dihedral : 18.536 114.569 1942 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.57 % Allowed : 16.51 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.28), residues: 830 helix: 0.16 (0.27), residues: 373 sheet: -0.17 (0.69), residues: 62 loop : -2.09 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 621 TYR 0.007 0.001 TYR A 766 PHE 0.030 0.002 PHE A 708 TRP 0.025 0.001 TRP A 382 HIS 0.004 0.001 HIS A 768 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 8588) covalent geometry : angle 0.55383 (11915) hydrogen bonds : bond 0.04110 ( 320) hydrogen bonds : angle 4.75490 ( 866) metal coordination : bond 0.01300 ( 7) metal coordination : angle 4.16654 ( 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 108 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.2366 (tpt) cc_final: 0.0246 (ptt) REVERT: A 245 MET cc_start: 0.1088 (ptt) cc_final: 0.0844 (ptt) REVERT: A 246 ARG cc_start: 0.4839 (mpt90) cc_final: 0.1680 (ptp90) REVERT: A 327 LEU cc_start: 0.1993 (OUTLIER) cc_final: 0.1587 (pp) REVERT: A 367 LYS cc_start: 0.5284 (mmtm) cc_final: 0.3429 (tptp) REVERT: A 689 LYS cc_start: 0.6914 (pptt) cc_final: 0.6400 (tptt) REVERT: A 824 MET cc_start: 0.4998 (mmm) cc_final: 0.4042 (mtp) outliers start: 19 outliers final: 7 residues processed: 100 average time/residue: 0.1247 time to fit residues: 16.2833 Evaluate side-chains 90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 772 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 83 optimal weight: 0.9980 chunk 71 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 66 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 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 = 0.4889 r_free = 0.4889 target = 0.200671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.190044 restraints weight = 30004.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.192134 restraints weight = 17970.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.193563 restraints weight = 11583.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.194630 restraints weight = 8065.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.195315 restraints weight = 5988.278| |-----------------------------------------------------------------------------| r_work (final): 0.4830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4009 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8595 Z= 0.100 Angle : 0.549 6.586 11917 Z= 0.283 Chirality : 0.037 0.213 1335 Planarity : 0.004 0.046 1270 Dihedral : 18.408 112.835 1942 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.35 % Allowed : 17.19 % 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 aren not related in a simple way. whole: -1.13 (0.29), residues: 830 helix: 0.42 (0.28), residues: 365 sheet: -0.67 (0.62), residues: 72 loop : -1.95 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 599 TYR 0.014 0.001 TYR A 882 PHE 0.031 0.002 PHE A 708 TRP 0.030 0.001 TRP A 382 HIS 0.003 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 8588) covalent geometry : angle 0.54655 (11915) hydrogen bonds : bond 0.04049 ( 320) hydrogen bonds : angle 4.62098 ( 866) metal coordination : bond 0.01295 ( 7) metal coordination : angle 3.95872 ( 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 95 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 238 MET cc_start: 0.2335 (tpt) cc_final: 0.0233 (ptt) REVERT: A 245 MET cc_start: 0.1136 (ptt) cc_final: 0.0892 (ptt) REVERT: A 246 ARG cc_start: 0.4851 (mpt90) cc_final: 0.1708 (ptp90) REVERT: A 327 LEU cc_start: 0.1734 (OUTLIER) cc_final: 0.1298 (pp) REVERT: A 367 LYS cc_start: 0.5160 (mmtm) cc_final: 0.3389 (tptp) REVERT: A 668 LYS cc_start: 0.6474 (tttm) cc_final: 0.6246 (tttm) REVERT: A 689 LYS cc_start: 0.6920 (pptt) cc_final: 0.6420 (tptt) REVERT: A 770 ARG cc_start: 0.3127 (mtt90) cc_final: 0.1825 (ptp-170) REVERT: A 824 MET cc_start: 0.5157 (mmm) cc_final: 0.3998 (mtp) outliers start: 10 outliers final: 7 residues processed: 91 average time/residue: 0.1152 time to fit residues: 13.8805 Evaluate side-chains 88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 772 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 6 optimal weight: 0.3980 chunk 75 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 9 optimal weight: 0.4980 chunk 85 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 364 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.198206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.187713 restraints weight = 29744.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.189903 restraints weight = 17414.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 74)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.191394 restraints weight = 11068.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.192371 restraints weight = 7588.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.193038 restraints weight = 5621.007| |-----------------------------------------------------------------------------| r_work (final): 0.4807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4129 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8595 Z= 0.130 Angle : 0.604 6.482 11917 Z= 0.312 Chirality : 0.039 0.260 1335 Planarity : 0.005 0.062 1270 Dihedral : 18.468 113.773 1942 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.89 % Allowed : 18.00 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.28), residues: 830 helix: 0.27 (0.27), residues: 363 sheet: -1.09 (0.62), residues: 72 loop : -2.03 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 599 TYR 0.011 0.001 TYR A 476 PHE 0.021 0.002 PHE A 674 TRP 0.023 0.001 TRP A 803 HIS 0.004 0.001 HIS A 768 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8588) covalent geometry : angle 0.60081 (11915) hydrogen bonds : bond 0.04509 ( 320) hydrogen bonds : angle 4.79514 ( 866) metal coordination : bond 0.01211 ( 7) metal coordination : angle 4.47058 ( 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 91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 245 MET cc_start: 0.1203 (ptt) cc_final: 0.0931 (ptt) REVERT: A 246 ARG cc_start: 0.4910 (mpt90) cc_final: 0.1705 (ptp90) REVERT: A 327 LEU cc_start: 0.1662 (OUTLIER) cc_final: 0.1092 (pp) REVERT: A 477 MET cc_start: 0.6527 (pmm) cc_final: 0.5959 (pmm) REVERT: A 668 LYS cc_start: 0.6905 (tttm) cc_final: 0.6485 (tttm) REVERT: A 689 LYS cc_start: 0.6937 (pptt) cc_final: 0.6529 (tptt) REVERT: A 770 ARG cc_start: 0.3343 (mtt90) cc_final: 0.1957 (ptp-170) REVERT: A 824 MET cc_start: 0.5030 (mmm) cc_final: 0.3897 (mtp) outliers start: 14 outliers final: 10 residues processed: 89 average time/residue: 0.1106 time to fit residues: 13.3224 Evaluate side-chains 86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 772 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 42 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 78 optimal weight: 0.0970 chunk 64 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 364 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.199644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.189321 restraints weight = 29910.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.191457 restraints weight = 17725.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.192837 restraints weight = 11307.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.193852 restraints weight = 7827.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.194523 restraints weight = 5810.817| |-----------------------------------------------------------------------------| r_work (final): 0.4824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4043 moved from start: 0.3744 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= 0.106 Angle : 0.567 6.802 11917 Z= 0.293 Chirality : 0.037 0.213 1335 Planarity : 0.005 0.053 1270 Dihedral : 18.376 113.147 1942 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.76 % Allowed : 18.00 % Favored : 80.24 % 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 aren not related in a simple way. whole: -1.23 (0.28), residues: 830 helix: 0.35 (0.27), residues: 366 sheet: -1.09 (0.59), residues: 82 loop : -1.94 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 599 TYR 0.013 0.001 TYR A 607 PHE 0.015 0.002 PHE A 708 TRP 0.021 0.001 TRP A 803 HIS 0.003 0.001 HIS A 768 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8588) covalent geometry : angle 0.56524 (11915) hydrogen bonds : bond 0.04157 ( 320) hydrogen bonds : angle 4.73254 ( 866) metal coordination : bond 0.01400 ( 7) metal coordination : angle 3.45781 ( 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: 13 poor density : 81 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 245 MET cc_start: 0.1230 (ptt) cc_final: 0.0964 (ptt) REVERT: A 246 ARG cc_start: 0.4937 (mpt90) cc_final: 0.1700 (ptp90) REVERT: A 327 LEU cc_start: 0.1897 (OUTLIER) cc_final: 0.1301 (pp) REVERT: A 367 LYS cc_start: 0.5362 (mmtm) cc_final: 0.3464 (tptp) REVERT: A 668 LYS cc_start: 0.6657 (tttm) cc_final: 0.6276 (tttm) REVERT: A 689 LYS cc_start: 0.6895 (pptt) cc_final: 0.6517 (tptt) REVERT: A 770 ARG cc_start: 0.3245 (mtt90) cc_final: 0.1754 (ptp-170) REVERT: A 824 MET cc_start: 0.5195 (OUTLIER) cc_final: 0.4089 (mtp) REVERT: A 882 TYR cc_start: 0.3577 (m-80) cc_final: 0.3204 (m-80) outliers start: 13 outliers final: 7 residues processed: 89 average time/residue: 0.1012 time to fit residues: 12.2438 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 : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 824 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 33 optimal weight: 0.0270 chunk 49 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 364 GLN A 555 ASN A 705 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.197145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.186667 restraints weight = 29415.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.188839 restraints weight = 17386.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.190229 restraints weight = 11024.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.191201 restraints weight = 7629.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.191855 restraints weight = 5666.442| |-----------------------------------------------------------------------------| r_work (final): 0.4797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4190 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8595 Z= 0.142 Angle : 0.632 7.282 11917 Z= 0.328 Chirality : 0.040 0.212 1335 Planarity : 0.006 0.061 1270 Dihedral : 18.434 113.709 1942 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.03 % Allowed : 18.00 % Favored : 79.97 % 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 aren not related in a simple way. whole: -1.53 (0.28), residues: 830 helix: 0.08 (0.27), residues: 364 sheet: -0.90 (0.67), residues: 62 loop : -2.11 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 599 TYR 0.014 0.002 TYR A 186 PHE 0.011 0.002 PHE A 243 TRP 0.046 0.002 TRP A 382 HIS 0.005 0.001 HIS A 768 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8588) covalent geometry : angle 0.62953 (11915) hydrogen bonds : bond 0.04736 ( 320) hydrogen bonds : angle 4.93411 ( 866) metal coordination : bond 0.00715 ( 7) metal coordination : angle 4.17605 ( 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 91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 245 MET cc_start: 0.1284 (ptt) cc_final: 0.1017 (ptt) REVERT: A 246 ARG cc_start: 0.4967 (mpt90) cc_final: 0.1696 (ptp90) REVERT: A 327 LEU cc_start: 0.1985 (OUTLIER) cc_final: 0.1241 (pp) REVERT: A 367 LYS cc_start: 0.5680 (mmtm) cc_final: 0.3423 (tptp) REVERT: A 668 LYS cc_start: 0.6827 (tttm) cc_final: 0.6477 (tttm) REVERT: A 689 LYS cc_start: 0.6953 (pptt) cc_final: 0.6597 (tptt) REVERT: A 770 ARG cc_start: 0.3261 (mtt90) cc_final: 0.1850 (ptp-170) REVERT: A 824 MET cc_start: 0.5023 (OUTLIER) cc_final: 0.3969 (mtp) REVERT: A 867 ILE cc_start: 0.2164 (mt) cc_final: 0.1785 (mt) outliers start: 15 outliers final: 10 residues processed: 87 average time/residue: 0.1066 time to fit residues: 12.6280 Evaluate side-chains 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 555 ASN Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 824 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 63 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 88 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.199099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.188945 restraints weight = 29938.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.191033 restraints weight = 17755.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.192475 restraints weight = 11294.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.193435 restraints weight = 7744.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.194053 restraints weight = 5731.992| |-----------------------------------------------------------------------------| r_work (final): 0.4829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4112 moved from start: 0.4030 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= 0.111 Angle : 0.585 7.209 11917 Z= 0.304 Chirality : 0.038 0.214 1335 Planarity : 0.005 0.054 1270 Dihedral : 18.384 113.682 1942 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.89 % Allowed : 17.86 % Favored : 80.24 % 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 aren not related in a simple way. whole: -1.37 (0.28), residues: 830 helix: 0.20 (0.27), residues: 366 sheet: -0.88 (0.68), residues: 62 loop : -2.02 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 599 TYR 0.014 0.002 TYR A 607 PHE 0.017 0.002 PHE A 708 TRP 0.034 0.001 TRP A 382 HIS 0.009 0.001 HIS A 556 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8588) covalent geometry : angle 0.58347 (11915) hydrogen bonds : bond 0.04339 ( 320) hydrogen bonds : angle 4.83950 ( 866) metal coordination : bond 0.00251 ( 7) metal coordination : angle 3.49573 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1864.88 seconds wall clock time: 32 minutes 51.96 seconds (1971.96 seconds total)