Starting phenix.real_space_refine on Thu Jul 2 09:51:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dtt_47165/07_2026/9dtt_47165.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dtt_47165/07_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_47165/07_2026/9dtt_47165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dtt_47165/07_2026/9dtt_47165.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dtt_47165/07_2026/9dtt_47165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dtt_47165/07_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-dev-6108/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: 1.52, per 1000 atoms: 0.18 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: 0.69 Conformation dependent library (CDL) restraints added in 276.7 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: 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: 1.09 Time building geometry restraints manager: 0.95 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 1.50e-02 4.44e+03 8.78e-01 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: 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=" 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=" C2 C B 14 " pdb=" N1 C B 14 " pdb=" C6 C B 14 " ideal model delta sigma weight residual 120.30 118.98 1.32 4.00e-01 6.25e+00 1.10e+01 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=" N9 G B 28 " pdb=" C4 G B 28 " pdb=" N3 G B 28 " ideal model delta sigma weight residual 126.00 127.61 -1.61 6.00e-01 2.78e+00 7.21e+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: 3.360 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.260 Find NCS groups from input model: 0.040 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:1.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.610 ------------------------------------------------------------------------------- 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= 0.114 Angle : 0.488 6.705 11917 Z= 0.314 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 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 0.00189 / 0.11 ( 8588) covalent geometry : angle 0.48648 / 0.31 (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 : 0.269 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: 0.6858 (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: 0.0981 time to fit residues: 15.9746 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 : 0.239 ------------------------------------------------------------------------------- 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 777 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.202671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.191303 restraints weight = 30423.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.193543 restraints weight = 17497.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.195217 restraints weight = 11194.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.196325 restraints weight = 7831.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.197048 restraints weight = 5902.579| |-----------------------------------------------------------------------------| r_work (final): 0.4843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3977 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8595 Z= 0.126 Angle : 0.577 10.917 11917 Z= 0.308 Chirality : 0.039 0.289 1335 Planarity : 0.004 0.034 1270 Dihedral : 18.415 113.836 1942 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.08 % Allowed : 7.98 % Favored : 90.93 % 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 are not related in a simple way. whole: -1.01 (0.28), residues: 830 helix: 0.52 (0.27), residues: 373 sheet: -0.68 (0.60), residues: 70 loop : -1.90 (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 0.021 0.002 PHE A 483 TRP 0.011 0.001 TRP A 700 HIS 0.008 0.002 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 8588) covalent geometry : angle 0.57111 / 0.31 (11915) hydrogen bonds : bond 0.05685 / 3.91 ( 320) hydrogen bonds : angle 5.17246 / 3.56 ( 866) metal coordination : bond 0.00703 / 0.29 ( 7) metal coordination : angle 6.46488 / 3.56 ( 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 98 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ARG cc_start: 0.4124 (mpt90) cc_final: 0.1345 (ptp90) REVERT: A 320 MET cc_start: 0.5687 (mpp) cc_final: 0.5479 (mpp) REVERT: A 534 ASP cc_start: 0.7117 (p0) cc_final: 0.6899 (p0) REVERT: A 599 ARG cc_start: 0.4798 (tpm170) cc_final: 0.4593 (tpt170) REVERT: A 668 LYS cc_start: 0.6549 (tttm) cc_final: 0.6242 (tttm) REVERT: A 689 LYS cc_start: 0.6906 (pptt) cc_final: 0.6194 (tptm) REVERT: A 824 MET cc_start: 0.4300 (mmm) cc_final: 0.3876 (mmm) outliers start: 8 outliers final: 1 residues processed: 93 average time/residue: 0.0888 time to fit residues: 11.1785 Evaluate side-chains 88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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: 30.0000 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 42 optimal weight: 0.0670 chunk 26 optimal weight: 0.7980 chunk 88 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 555 ASN ** 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 = 0.4915 r_free = 0.4915 target = 0.202415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.191402 restraints weight = 30169.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.193487 restraints weight = 17468.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.194940 restraints weight = 11213.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.196021 restraints weight = 7919.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.196761 restraints weight = 6058.483| |-----------------------------------------------------------------------------| r_work (final): 0.4852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4037 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8595 Z= 0.112 Angle : 0.532 9.363 11917 Z= 0.286 Chirality : 0.038 0.219 1335 Planarity : 0.004 0.051 1270 Dihedral : 18.408 116.389 1942 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.08 % Allowed : 10.01 % Favored : 88.90 % 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 are not related in a simple way. whole: -1.04 (0.28), residues: 830 helix: 0.54 (0.27), residues: 374 sheet: -0.65 (0.64), residues: 62 loop : -1.96 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 362 TYR 0.011 0.001 TYR A 476 PHE 0.027 0.002 PHE A 708 TRP 0.011 0.001 TRP A 803 HIS 0.005 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 8588) covalent geometry : angle 0.52589 / 0.29 (11915) hydrogen bonds : bond 0.04993 / 3.43 ( 320) hydrogen bonds : angle 5.00136 / 3.40 ( 866) metal coordination : bond 0.01250 / 0.69 ( 7) metal coordination : angle 6.25838 / 3.30 ( 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 101 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.3138 (tt0) cc_final: 0.2894 (mp0) REVERT: A 245 MET cc_start: 0.0236 (ptt) cc_final: 0.0005 (ptt) REVERT: A 246 ARG cc_start: 0.3993 (mpt90) cc_final: 0.1241 (ptp90) REVERT: A 367 LYS cc_start: 0.5908 (mmtm) cc_final: 0.5602 (mmtm) REVERT: A 668 LYS cc_start: 0.6843 (tttm) cc_final: 0.6515 (tttm) REVERT: A 689 LYS cc_start: 0.6961 (pptt) cc_final: 0.6249 (tptt) REVERT: A 770 ARG cc_start: 0.3412 (mtt90) cc_final: 0.2089 (ptp-170) REVERT: A 824 MET cc_start: 0.4791 (mmm) cc_final: 0.3600 (mtp) outliers start: 8 outliers final: 4 residues processed: 98 average time/residue: 0.0852 time to fit residues: 11.4182 Evaluate side-chains 88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 373 LEU 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: 0.7980 chunk 21 optimal weight: 0.0170 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- 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** A 742 GLN ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.202118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.191462 restraints weight = 30683.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.193520 restraints weight = 17838.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.194966 restraints weight = 11528.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.196053 restraints weight = 8165.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.196747 restraints weight = 6172.458| |-----------------------------------------------------------------------------| r_work (final): 0.4841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3976 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8595 Z= 0.111 Angle : 0.550 9.218 11917 Z= 0.292 Chirality : 0.038 0.219 1335 Planarity : 0.004 0.061 1270 Dihedral : 18.379 116.235 1942 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.08 % Allowed : 11.91 % Favored : 87.01 % 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: -1.03 (0.28), residues: 830 helix: 0.53 (0.27), residues: 376 sheet: -0.66 (0.65), residues: 62 loop : -1.96 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 362 TYR 0.010 0.001 TYR A 452 PHE 0.033 0.002 PHE A 708 TRP 0.019 0.001 TRP A 813 HIS 0.004 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 8588) covalent geometry : angle 0.54558 / 0.29 (11915) hydrogen bonds : bond 0.04832 / 3.29 ( 320) hydrogen bonds : angle 4.91494 / 3.33 ( 866) metal coordination : bond 0.00935 / 0.52 ( 7) metal coordination : angle 5.24440 / 2.76 ( 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 96 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.0735 (ptt) cc_final: 0.0416 (ptt) REVERT: A 246 ARG cc_start: 0.4427 (mpt90) cc_final: 0.1586 (ptp90) REVERT: A 367 LYS cc_start: 0.5697 (mmtm) cc_final: 0.5157 (mmtm) REVERT: A 477 MET cc_start: 0.5956 (pmm) cc_final: 0.5581 (pmm) REVERT: A 689 LYS cc_start: 0.6837 (pptt) cc_final: 0.6277 (tptt) REVERT: A 770 ARG cc_start: 0.3300 (mtt90) cc_final: 0.1968 (ptp-170) REVERT: A 824 MET cc_start: 0.4959 (mmm) cc_final: 0.3883 (mtp) outliers start: 8 outliers final: 6 residues processed: 93 average time/residue: 0.0937 time to fit residues: 11.7382 Evaluate side-chains 85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 37 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 66 optimal weight: 0.0010 chunk 90 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN ** 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 = 0.4913 r_free = 0.4913 target = 0.202506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.191492 restraints weight = 30404.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.193657 restraints weight = 17640.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.195174 restraints weight = 11259.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.196295 restraints weight = 7838.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.196993 restraints weight = 5875.509| |-----------------------------------------------------------------------------| r_work (final): 0.4843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3994 moved from start: 0.1900 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= 0.107 Angle : 0.553 9.186 11917 Z= 0.291 Chirality : 0.038 0.221 1335 Planarity : 0.004 0.080 1270 Dihedral : 18.357 116.461 1942 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.22 % Allowed : 13.94 % Favored : 84.84 % 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: -1.02 (0.28), residues: 830 helix: 0.56 (0.27), residues: 376 sheet: -0.66 (0.67), residues: 62 loop : -1.97 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.016 0.001 TYR A 882 PHE 0.013 0.001 PHE A 674 TRP 0.039 0.001 TRP A 419 HIS 0.003 0.001 HIS A 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 8588) covalent geometry : angle 0.54941 / 0.29 (11915) hydrogen bonds : bond 0.04607 / 3.16 ( 320) hydrogen bonds : angle 4.88606 / 3.30 ( 866) metal coordination : bond 0.01036 / 0.59 ( 7) metal coordination : angle 4.59776 / 2.42 ( 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 97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.1399 (tpt) cc_final: -0.0239 (ptt) REVERT: A 245 MET cc_start: 0.0699 (ptt) cc_final: 0.0366 (ptt) REVERT: A 246 ARG cc_start: 0.4384 (mpt90) cc_final: 0.1535 (ptp90) REVERT: A 367 LYS cc_start: 0.5792 (mmtm) cc_final: 0.4358 (tptp) REVERT: A 477 MET cc_start: 0.6092 (pmm) cc_final: 0.5692 (pmm) REVERT: A 689 LYS cc_start: 0.6947 (pptt) cc_final: 0.6341 (tptt) REVERT: A 770 ARG cc_start: 0.3266 (mtt90) cc_final: 0.1922 (ptp-170) REVERT: A 797 ILE cc_start: 0.4650 (pt) cc_final: 0.4417 (mm) REVERT: A 824 MET cc_start: 0.4966 (mmm) cc_final: 0.3835 (mtp) outliers start: 9 outliers final: 6 residues processed: 94 average time/residue: 0.0983 time to fit residues: 12.4032 Evaluate side-chains 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 68 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 29 optimal weight: 0.0570 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.7904 ------------------------------------------------------------------------------- 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 = 0.4919 r_free = 0.4919 target = 0.203003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.192090 restraints weight = 30000.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.194086 restraints weight = 17517.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.195589 restraints weight = 11370.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.196402 restraints weight = 8005.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.197360 restraints weight = 6267.128| |-----------------------------------------------------------------------------| r_work (final): 0.4848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3960 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8595 Z= 0.104 Angle : 0.551 9.071 11917 Z= 0.291 Chirality : 0.038 0.223 1335 Planarity : 0.004 0.070 1270 Dihedral : 18.320 116.458 1942 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.49 % Allowed : 14.21 % Favored : 84.30 % 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: -1.05 (0.28), residues: 830 helix: 0.55 (0.27), residues: 378 sheet: -0.70 (0.66), residues: 62 loop : -2.01 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 362 TYR 0.010 0.001 TYR A 882 PHE 0.010 0.001 PHE A 674 TRP 0.019 0.001 TRP A 803 HIS 0.003 0.001 HIS A 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 8588) covalent geometry : angle 0.54898 / 0.29 (11915) hydrogen bonds : bond 0.04467 / 3.06 ( 320) hydrogen bonds : angle 4.79427 / 3.24 ( 866) metal coordination : bond 0.01155 / 0.66 ( 7) metal coordination : angle 4.02030 / 2.12 ( 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 95 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 238 MET cc_start: 0.1431 (tpt) cc_final: -0.0232 (ptt) REVERT: A 245 MET cc_start: 0.0780 (ptt) cc_final: 0.0459 (ptt) REVERT: A 246 ARG cc_start: 0.4440 (mpt90) cc_final: 0.1584 (ptp90) REVERT: A 367 LYS cc_start: 0.5658 (mmtm) cc_final: 0.4361 (tptp) REVERT: A 534 ASP cc_start: 0.7175 (p0) cc_final: 0.6964 (p0) REVERT: A 689 LYS cc_start: 0.6951 (pptt) cc_final: 0.6336 (tptt) REVERT: A 770 ARG cc_start: 0.3218 (mtt90) cc_final: 0.1907 (ptp-170) REVERT: A 824 MET cc_start: 0.4997 (mmm) cc_final: 0.3926 (mtp) outliers start: 11 outliers final: 6 residues processed: 91 average time/residue: 0.0989 time to fit residues: 12.1352 Evaluate side-chains 84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 83 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 26 optimal weight: 2.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.200423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.189606 restraints weight = 30354.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.191661 restraints weight = 17632.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.193062 restraints weight = 11427.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.194180 restraints weight = 8016.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.194844 restraints weight = 6017.957| |-----------------------------------------------------------------------------| r_work (final): 0.4820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4092 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8595 Z= 0.149 Angle : 0.607 9.769 11917 Z= 0.320 Chirality : 0.040 0.276 1335 Planarity : 0.005 0.056 1270 Dihedral : 18.392 117.017 1942 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.03 % Allowed : 13.94 % Favored : 84.03 % 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: 0.38 (0.27), residues: 371 sheet: -0.87 (0.67), residues: 62 loop : -2.10 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 599 TYR 0.013 0.002 TYR A 186 PHE 0.018 0.002 PHE A 708 TRP 0.020 0.001 TRP A 803 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 8588) covalent geometry : angle 0.60358 / 0.32 (11915) hydrogen bonds : bond 0.04808 / 3.26 ( 320) hydrogen bonds : angle 4.90665 / 3.31 ( 866) metal coordination : bond 0.00841 / 0.44 ( 7) metal coordination : angle 5.26845 / 2.78 ( 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 97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.0939 (ptt) cc_final: 0.0620 (ptt) REVERT: A 246 ARG cc_start: 0.4529 (mpt90) cc_final: 0.1623 (ptp90) REVERT: A 534 ASP cc_start: 0.7252 (p0) cc_final: 0.6974 (p0) REVERT: A 689 LYS cc_start: 0.7003 (pptt) cc_final: 0.6329 (tptt) REVERT: A 770 ARG cc_start: 0.3324 (mtt90) cc_final: 0.2032 (ptp-170) REVERT: A 824 MET cc_start: 0.5162 (mmm) cc_final: 0.3924 (mtp) outliers start: 15 outliers final: 8 residues processed: 94 average time/residue: 0.1086 time to fit residues: 13.7725 Evaluate side-chains 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 359 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 708 PHE 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: 0.1980 chunk 75 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 10 optimal weight: 0.0370 chunk 80 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.202183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.191261 restraints weight = 30299.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.193305 restraints weight = 17763.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.194813 restraints weight = 11425.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.195881 restraints weight = 8012.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.196572 restraints weight = 6053.917| |-----------------------------------------------------------------------------| r_work (final): 0.4845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4049 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 8595 Z= 0.105 Angle : 0.574 9.332 11917 Z= 0.299 Chirality : 0.038 0.250 1335 Planarity : 0.004 0.053 1270 Dihedral : 18.327 116.760 1942 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.22 % Allowed : 14.61 % Favored : 84.17 % 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: -1.14 (0.28), residues: 830 helix: 0.48 (0.27), residues: 377 sheet: -0.67 (0.67), residues: 62 loop : -2.06 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 599 TYR 0.012 0.002 TYR A 882 PHE 0.014 0.001 PHE A 708 TRP 0.021 0.001 TRP A 803 HIS 0.003 0.001 HIS A 711 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 8588) covalent geometry : angle 0.57174 / 0.30 (11915) hydrogen bonds : bond 0.04466 / 3.08 ( 320) hydrogen bonds : angle 4.83809 / 3.29 ( 866) metal coordination : bond 0.01095 / 0.62 ( 7) metal coordination : angle 3.53826 / 1.86 ( 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 90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 245 MET cc_start: 0.0733 (ptt) cc_final: 0.0436 (ptt) REVERT: A 246 ARG cc_start: 0.4434 (mpt90) cc_final: 0.1506 (ptp90) REVERT: A 367 LYS cc_start: 0.5806 (mmtm) cc_final: 0.4307 (tptp) REVERT: A 689 LYS cc_start: 0.7035 (pptt) cc_final: 0.6308 (tptt) REVERT: A 770 ARG cc_start: 0.3270 (mtt90) cc_final: 0.1950 (ptp-170) REVERT: A 824 MET cc_start: 0.5201 (mmm) cc_final: 0.4011 (mtp) outliers start: 9 outliers final: 7 residues processed: 87 average time/residue: 0.1001 time to fit residues: 11.6984 Evaluate side-chains 81 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 42 optimal weight: 0.4980 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 64 optimal weight: 0.0670 chunk 53 optimal weight: 0.8980 chunk 79 optimal weight: 0.0980 chunk 46 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.3118 ------------------------------------------------------------------------------- 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 = 0.4911 r_free = 0.4911 target = 0.203100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.193060 restraints weight = 30415.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.195323 restraints weight = 18043.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.196341 restraints weight = 11388.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.197222 restraints weight = 8145.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.197774 restraints weight = 6114.781| |-----------------------------------------------------------------------------| r_work (final): 0.4847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3937 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8595 Z= 0.105 Angle : 0.578 11.036 11917 Z= 0.300 Chirality : 0.038 0.223 1335 Planarity : 0.004 0.047 1270 Dihedral : 18.224 115.713 1942 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.08 % Allowed : 14.88 % Favored : 84.03 % 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: -1.08 (0.28), residues: 830 helix: 0.48 (0.27), residues: 380 sheet: -0.65 (0.66), residues: 62 loop : -2.00 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 599 TYR 0.013 0.001 TYR A 766 PHE 0.022 0.002 PHE A 708 TRP 0.020 0.001 TRP A 803 HIS 0.003 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 8588) covalent geometry : angle 0.57643 / 0.30 (11915) hydrogen bonds : bond 0.04215 / 2.90 ( 320) hydrogen bonds : angle 4.78076 / 3.24 ( 866) metal coordination : bond 0.01239 / 0.71 ( 7) metal coordination : angle 2.81918 / 1.48 ( 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 89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 245 MET cc_start: 0.0913 (ptt) cc_final: 0.0555 (ptt) REVERT: A 246 ARG cc_start: 0.4519 (mpt90) cc_final: 0.1614 (ptp90) REVERT: A 367 LYS cc_start: 0.5597 (mmtm) cc_final: 0.4433 (tptp) REVERT: A 689 LYS cc_start: 0.6841 (pptt) cc_final: 0.6279 (tptt) REVERT: A 770 ARG cc_start: 0.3216 (mtt90) cc_final: 0.1987 (ptp-170) REVERT: A 824 MET cc_start: 0.5159 (mmm) cc_final: 0.4089 (mtp) outliers start: 8 outliers final: 7 residues processed: 88 average time/residue: 0.1134 time to fit residues: 13.5610 Evaluate side-chains 80 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 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 72 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.202655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.192199 restraints weight = 30086.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.194228 restraints weight = 18012.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.195640 restraints weight = 11672.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.196698 restraints weight = 8224.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.197411 restraints weight = 6226.461| |-----------------------------------------------------------------------------| r_work (final): 0.4845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3942 moved from start: 0.2600 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= 0.111 Angle : 0.598 9.982 11917 Z= 0.310 Chirality : 0.039 0.315 1335 Planarity : 0.004 0.050 1270 Dihedral : 18.187 115.398 1942 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.08 % Allowed : 15.16 % Favored : 83.76 % 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: -1.09 (0.28), residues: 830 helix: 0.53 (0.27), residues: 374 sheet: -0.74 (0.64), residues: 62 loop : -2.02 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 599 TYR 0.009 0.001 TYR A 186 PHE 0.026 0.002 PHE A 708 TRP 0.054 0.002 TRP A 419 HIS 0.006 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 8588) covalent geometry : angle 0.59610 / 0.31 (11915) hydrogen bonds : bond 0.04240 / 2.92 ( 320) hydrogen bonds : angle 4.70828 / 3.18 ( 866) metal coordination : bond 0.01112 / 0.63 ( 7) metal coordination : angle 3.26428 / 1.72 ( 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 83 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 245 MET cc_start: 0.0940 (ptt) cc_final: 0.0577 (ptt) REVERT: A 246 ARG cc_start: 0.4581 (mpt90) cc_final: 0.1677 (ptp90) REVERT: A 367 LYS cc_start: 0.5584 (mmtm) cc_final: 0.4410 (tptp) REVERT: A 689 LYS cc_start: 0.6818 (pptt) cc_final: 0.6339 (tptt) REVERT: A 770 ARG cc_start: 0.3251 (mtt90) cc_final: 0.1946 (ptp-170) REVERT: A 824 MET cc_start: 0.5203 (mmm) cc_final: 0.4047 (mtp) outliers start: 8 outliers final: 8 residues processed: 82 average time/residue: 0.0979 time to fit residues: 10.8351 Evaluate side-chains 81 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 723 VAL 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: 1.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 chunk 57 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN A 556 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 = 0.4884 r_free = 0.4884 target = 0.200307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.189932 restraints weight = 30400.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.192000 restraints weight = 18144.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.193392 restraints weight = 11637.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.194432 restraints weight = 8161.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.195079 restraints weight = 6141.875| |-----------------------------------------------------------------------------| r_work (final): 0.4827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4080 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8595 Z= 0.137 Angle : 0.626 10.412 11917 Z= 0.325 Chirality : 0.040 0.220 1335 Planarity : 0.005 0.048 1270 Dihedral : 18.209 115.624 1942 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.22 % Allowed : 15.02 % Favored : 83.76 % 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: -1.24 (0.28), residues: 830 helix: 0.40 (0.27), residues: 374 sheet: -0.98 (0.58), residues: 72 loop : -2.08 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 599 TYR 0.013 0.002 TYR A 766 PHE 0.018 0.002 PHE A 708 TRP 0.022 0.002 TRP A 419 HIS 0.007 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 8588) covalent geometry : angle 0.62357 / 0.32 (11915) hydrogen bonds : bond 0.04608 / 3.17 ( 320) hydrogen bonds : angle 4.85203 / 3.28 ( 866) metal coordination : bond 0.00634 / 0.33 ( 7) metal coordination : angle 4.58729 / 2.42 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1659.93 seconds wall clock time: 29 minutes 19.72 seconds (1759.72 seconds total)