Starting phenix.real_space_refine on Wed Jan 15 09:07:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dtt_47165/01_2025/9dtt_47165.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dtt_47165/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dtt_47165/01_2025/9dtt_47165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dtt_47165/01_2025/9dtt_47165.map" model { file = "/net/cci-nas-00/data/ceres_data/9dtt_47165/01_2025/9dtt_47165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dtt_47165/01_2025/9dtt_47165.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 5.74, per 1000 atoms: 0.69 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: 2.46 Conformation dependent library (CDL) restraints added in 797.1 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: 2.98 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: 2.66 Time building geometry restraints manager: 2.63 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: 3.330 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.960 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.840 ------------------------------------------------------------------------------- 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 8588 Z= 0.122 Angle : 0.486 6.705 11915 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (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 TRP 0.024 0.001 TRP A 220 HIS 0.005 0.001 HIS A 768 PHE 0.012 0.001 PHE A 178 TYR 0.011 0.001 TYR A 452 ARG 0.003 0.000 ARG A 769 *********************** 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 : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ARG cc_start: 0.3731 (mpt90) cc_final: 0.1068 (ptp90) REVERT: A 367 LYS cc_start: 0.5634 (mmtm) cc_final: 0.5224 (mmtm) REVERT: A 534 ASP cc_start: 0.7143 (p0) cc_final: 0.6856 (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: 0.2761 time to fit residues: 44.2208 Evaluate side-chains 90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.0050 chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 43 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- 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 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 GLN A 777 ASN ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.203500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.192603 restraints weight = 30046.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.194691 restraints weight = 17516.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.196230 restraints weight = 11388.082| |-----------------------------------------------------------------------------| r_work (final): 0.4833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3996 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8588 Z= 0.140 Angle : 0.543 9.062 11915 Z= 0.279 Chirality : 0.037 0.218 1335 Planarity : 0.004 0.041 1270 Dihedral : 18.310 114.429 1942 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.81 % Allowed : 7.85 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.29), residues: 830 helix: 0.69 (0.28), residues: 377 sheet: -0.60 (0.61), residues: 72 loop : -1.82 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 220 HIS 0.005 0.001 HIS A 712 PHE 0.011 0.002 PHE A 483 TYR 0.011 0.001 TYR A 476 ARG 0.003 0.000 ARG A 362 *********************** 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 102 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ARG cc_start: 0.3815 (mpt90) cc_final: 0.1115 (ptp90) REVERT: A 534 ASP cc_start: 0.7099 (p0) cc_final: 0.6853 (p0) REVERT: A 668 LYS cc_start: 0.6508 (tttm) cc_final: 0.6227 (tttm) REVERT: A 689 LYS cc_start: 0.7008 (pptt) cc_final: 0.6304 (tptt) REVERT: A 824 MET cc_start: 0.4559 (mmm) cc_final: 0.3880 (mmm) outliers start: 6 outliers final: 1 residues processed: 98 average time/residue: 0.2690 time to fit residues: 34.6238 Evaluate side-chains 84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 78 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.4852 r_free = 0.4852 target = 0.196840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.185674 restraints weight = 30301.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.187898 restraints weight = 17310.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.189438 restraints weight = 11031.710| |-----------------------------------------------------------------------------| r_work (final): 0.4767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4317 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 8588 Z= 0.286 Angle : 0.711 8.489 11915 Z= 0.372 Chirality : 0.043 0.219 1335 Planarity : 0.006 0.058 1270 Dihedral : 18.770 118.013 1942 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.44 % Allowed : 10.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.28), residues: 830 helix: -0.05 (0.27), residues: 366 sheet: -0.98 (0.65), residues: 62 loop : -2.07 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 497 HIS 0.008 0.002 HIS A 712 PHE 0.022 0.003 PHE A 674 TYR 0.019 0.002 TYR A 476 ARG 0.007 0.001 ARG A 621 *********************** 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 112 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 ARG cc_start: 0.4299 (mpt90) cc_final: 0.1272 (ttp80) REVERT: A 689 LYS cc_start: 0.7013 (pptt) cc_final: 0.6346 (tptt) REVERT: A 770 ARG cc_start: 0.3440 (mtt90) cc_final: 0.2277 (ptp-170) REVERT: A 824 MET cc_start: 0.4773 (mmm) cc_final: 0.3626 (mtp) outliers start: 18 outliers final: 8 residues processed: 106 average time/residue: 0.2692 time to fit residues: 37.1659 Evaluate side-chains 86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** ** 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 = 0.4809 r_free = 0.4809 target = 0.192656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.181708 restraints weight = 29704.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.183837 restraints weight = 16806.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.185378 restraints weight = 10563.003| |-----------------------------------------------------------------------------| r_work (final): 0.4725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4478 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 8588 Z= 0.331 Angle : 0.826 8.085 11915 Z= 0.431 Chirality : 0.047 0.225 1335 Planarity : 0.006 0.063 1270 Dihedral : 19.466 119.922 1942 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.25 % Allowed : 15.16 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.27), residues: 830 helix: -0.77 (0.26), residues: 359 sheet: -0.91 (0.75), residues: 52 loop : -2.31 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 497 HIS 0.010 0.002 HIS A 306 PHE 0.023 0.003 PHE A 612 TYR 0.025 0.003 TYR A 476 ARG 0.009 0.001 ARG A 749 *********************** 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 116 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 246 ARG cc_start: 0.4814 (mpt90) cc_final: 0.1549 (ttp80) REVERT: A 515 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6488 (mp) REVERT: A 689 LYS cc_start: 0.6950 (pptt) cc_final: 0.6458 (tptt) REVERT: A 770 ARG cc_start: 0.3572 (mtt90) cc_final: 0.2603 (ptp-170) REVERT: A 824 MET cc_start: 0.5010 (mmm) cc_final: 0.4066 (mtp) outliers start: 24 outliers final: 11 residues processed: 108 average time/residue: 0.2682 time to fit residues: 38.1256 Evaluate side-chains 93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 813 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 64 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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** ** 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 = 0.4833 r_free = 0.4833 target = 0.194488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.183576 restraints weight = 29828.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.185666 restraints weight = 17248.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.187126 restraints weight = 10945.015| |-----------------------------------------------------------------------------| r_work (final): 0.4743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4357 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8588 Z= 0.213 Angle : 0.667 7.558 11915 Z= 0.351 Chirality : 0.041 0.223 1335 Planarity : 0.005 0.054 1270 Dihedral : 19.194 118.835 1942 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.59 % Favored : 92.29 % Rotamer: Outliers : 2.84 % Allowed : 17.73 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.27), residues: 830 helix: -0.65 (0.26), residues: 366 sheet: -0.84 (0.67), residues: 64 loop : -2.31 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 700 HIS 0.006 0.001 HIS A 768 PHE 0.017 0.002 PHE A 674 TYR 0.015 0.002 TYR A 882 ARG 0.006 0.001 ARG A 621 *********************** 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 111 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 689 LYS cc_start: 0.6942 (pptt) cc_final: 0.6520 (tptt) REVERT: A 770 ARG cc_start: 0.3565 (mtt90) cc_final: 0.2663 (ptp-170) REVERT: A 824 MET cc_start: 0.5106 (mmm) cc_final: 0.4169 (mtp) outliers start: 21 outliers final: 7 residues processed: 107 average time/residue: 0.2539 time to fit residues: 35.8225 Evaluate side-chains 91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 309 TYR Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 813 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 87 optimal weight: 9.9990 chunk 25 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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** A 821 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.197875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.186937 restraints weight = 29783.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.189136 restraints weight = 17107.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.190684 restraints weight = 10779.672| |-----------------------------------------------------------------------------| r_work (final): 0.4773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4234 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8588 Z= 0.156 Angle : 0.601 7.322 11915 Z= 0.311 Chirality : 0.038 0.222 1335 Planarity : 0.005 0.055 1270 Dihedral : 18.882 116.597 1942 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.02 % Favored : 93.86 % Rotamer: Outliers : 2.57 % Allowed : 18.27 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.28), residues: 830 helix: -0.36 (0.26), residues: 377 sheet: -0.84 (0.62), residues: 72 loop : -2.25 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 220 HIS 0.004 0.001 HIS A 768 PHE 0.012 0.002 PHE A 708 TYR 0.011 0.001 TYR A 607 ARG 0.008 0.001 ARG A 739 *********************** 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 114 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 LYS cc_start: 0.5426 (mmtm) cc_final: 0.3305 (tptp) REVERT: A 477 MET cc_start: 0.6378 (pmm) cc_final: 0.5855 (pmm) REVERT: A 689 LYS cc_start: 0.6983 (pptt) cc_final: 0.6612 (tptt) REVERT: A 770 ARG cc_start: 0.3482 (mtt90) cc_final: 0.2285 (ptp-170) REVERT: A 824 MET cc_start: 0.5261 (mmm) cc_final: 0.4090 (mtp) outliers start: 19 outliers final: 13 residues processed: 107 average time/residue: 0.2552 time to fit residues: 36.7063 Evaluate side-chains 100 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 335 VAL Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 813 TRP Chi-restraints excluded: chain A residue 830 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 2 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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** ** A 768 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 = 0.4828 r_free = 0.4828 target = 0.194446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.183803 restraints weight = 29783.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.185953 restraints weight = 17090.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.187527 restraints weight = 10799.484| |-----------------------------------------------------------------------------| r_work (final): 0.4742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4382 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8588 Z= 0.235 Angle : 0.691 8.599 11915 Z= 0.360 Chirality : 0.042 0.262 1335 Planarity : 0.006 0.056 1270 Dihedral : 19.040 117.432 1942 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.28 % Favored : 90.60 % Rotamer: Outliers : 3.11 % Allowed : 18.81 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.27), residues: 830 helix: -0.47 (0.26), residues: 368 sheet: -1.23 (0.63), residues: 64 loop : -2.30 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 382 HIS 0.006 0.001 HIS A 634 PHE 0.016 0.002 PHE A 674 TYR 0.016 0.002 TYR A 186 ARG 0.006 0.001 ARG A 621 *********************** 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 109 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 VAL cc_start: 0.4652 (OUTLIER) cc_final: 0.4306 (t) REVERT: A 689 LYS cc_start: 0.7083 (pptt) cc_final: 0.6723 (tptt) REVERT: A 718 MET cc_start: 0.6361 (ptp) cc_final: 0.5923 (ptp) REVERT: A 770 ARG cc_start: 0.3508 (mtt90) cc_final: 0.2437 (ptp-170) REVERT: A 824 MET cc_start: 0.5303 (OUTLIER) cc_final: 0.4126 (mtp) outliers start: 23 outliers final: 14 residues processed: 105 average time/residue: 0.2342 time to fit residues: 32.8507 Evaluate side-chains 98 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 335 VAL 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 577 VAL Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 612 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 57 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 24 optimal weight: 0.0060 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 85 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 ** 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 = 0.4883 r_free = 0.4883 target = 0.199434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.188934 restraints weight = 30172.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.191130 restraints weight = 17595.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.192663 restraints weight = 11140.368| |-----------------------------------------------------------------------------| r_work (final): 0.4797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4155 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8588 Z= 0.147 Angle : 0.592 7.153 11915 Z= 0.307 Chirality : 0.038 0.242 1335 Planarity : 0.005 0.053 1270 Dihedral : 18.848 114.877 1942 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.54 % Favored : 94.34 % Rotamer: Outliers : 2.17 % Allowed : 19.08 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.28), residues: 830 helix: 0.07 (0.27), residues: 371 sheet: -1.23 (0.56), residues: 82 loop : -2.04 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 220 HIS 0.004 0.001 HIS A 712 PHE 0.008 0.001 PHE A 674 TYR 0.014 0.001 TYR A 882 ARG 0.005 0.000 ARG A 212 *********************** 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 106 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 367 LYS cc_start: 0.5262 (mmtm) cc_final: 0.3323 (tptp) REVERT: A 668 LYS cc_start: 0.6817 (tttm) cc_final: 0.6468 (tttm) REVERT: A 689 LYS cc_start: 0.7063 (pptt) cc_final: 0.6621 (tptt) REVERT: A 718 MET cc_start: 0.6250 (ptp) cc_final: 0.5851 (ptp) REVERT: A 770 ARG cc_start: 0.3333 (mtt90) cc_final: 0.2211 (ptp-170) REVERT: A 809 MET cc_start: 0.1356 (mmm) cc_final: 0.0446 (mmm) REVERT: A 824 MET cc_start: 0.5118 (OUTLIER) cc_final: 0.4050 (mtp) outliers start: 16 outliers final: 5 residues processed: 101 average time/residue: 0.2584 time to fit residues: 34.6956 Evaluate side-chains 94 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 746 TRP Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 824 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 64 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 0.0670 chunk 88 optimal weight: 9.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4851 r_free = 0.4851 target = 0.196731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.186324 restraints weight = 30168.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.188552 restraints weight = 17535.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.190145 restraints weight = 11027.183| |-----------------------------------------------------------------------------| r_work (final): 0.4767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4275 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8588 Z= 0.185 Angle : 0.637 8.336 11915 Z= 0.332 Chirality : 0.039 0.215 1335 Planarity : 0.005 0.056 1270 Dihedral : 18.830 114.656 1942 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.47 % Favored : 92.41 % Rotamer: Outliers : 2.17 % Allowed : 20.03 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.28), residues: 830 helix: -0.11 (0.27), residues: 371 sheet: -0.99 (0.62), residues: 72 loop : -2.14 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 382 HIS 0.004 0.001 HIS A 768 PHE 0.028 0.002 PHE A 674 TYR 0.014 0.002 TYR A 186 ARG 0.008 0.000 ARG A 621 *********************** 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 102 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 VAL cc_start: 0.4276 (OUTLIER) cc_final: 0.4048 (t) REVERT: A 367 LYS cc_start: 0.5588 (mmtm) cc_final: 0.5050 (mptt) REVERT: A 689 LYS cc_start: 0.6991 (pptt) cc_final: 0.6731 (tptt) REVERT: A 770 ARG cc_start: 0.3353 (mtt90) cc_final: 0.2138 (ptp-170) REVERT: A 824 MET cc_start: 0.5211 (OUTLIER) cc_final: 0.4089 (mtp) outliers start: 16 outliers final: 9 residues processed: 97 average time/residue: 0.2397 time to fit residues: 31.1809 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 : 0.936 ------------------------------------------------------------------------------- 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 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 746 TRP 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 50 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4867 r_free = 0.4867 target = 0.198019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.187934 restraints weight = 30077.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.190103 restraints weight = 17415.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.191482 restraints weight = 10914.028| |-----------------------------------------------------------------------------| r_work (final): 0.4786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4207 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8588 Z= 0.159 Angle : 0.610 7.832 11915 Z= 0.316 Chirality : 0.039 0.217 1335 Planarity : 0.005 0.056 1270 Dihedral : 18.758 114.638 1942 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.51 % Favored : 93.37 % Rotamer: Outliers : 2.03 % Allowed : 20.43 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.28), residues: 830 helix: -0.01 (0.27), residues: 371 sheet: -1.08 (0.62), residues: 72 loop : -2.09 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 382 HIS 0.004 0.001 HIS A 712 PHE 0.014 0.002 PHE A 674 TYR 0.013 0.001 TYR A 882 ARG 0.004 0.000 ARG A 482 ********************** 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 99 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 VAL cc_start: 0.4097 (OUTLIER) cc_final: 0.3684 (t) REVERT: A 367 LYS cc_start: 0.5435 (mmtm) cc_final: 0.3275 (tmtt) REVERT: A 668 LYS cc_start: 0.6875 (tttm) cc_final: 0.6502 (tttm) REVERT: A 689 LYS cc_start: 0.7162 (pptt) cc_final: 0.6774 (tptt) REVERT: A 770 ARG cc_start: 0.3252 (mtt90) cc_final: 0.1822 (ptp-170) REVERT: A 824 MET cc_start: 0.5178 (OUTLIER) cc_final: 0.4084 (mtp) outliers start: 15 outliers final: 11 residues processed: 94 average time/residue: 0.2502 time to fit residues: 31.4628 Evaluate side-chains 96 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 335 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 746 TRP 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 39 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 622 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 = 0.4879 r_free = 0.4879 target = 0.199287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.189230 restraints weight = 30357.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.191476 restraints weight = 17758.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.192896 restraints weight = 11089.335| |-----------------------------------------------------------------------------| r_work (final): 0.4802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4160 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8588 Z= 0.147 Angle : 0.589 10.312 11915 Z= 0.303 Chirality : 0.038 0.213 1335 Planarity : 0.005 0.054 1270 Dihedral : 18.568 112.827 1942 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.78 % Favored : 94.10 % Rotamer: Outliers : 2.30 % Allowed : 20.30 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.29), residues: 830 helix: 0.23 (0.27), residues: 371 sheet: -1.13 (0.62), residues: 74 loop : -1.95 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 303 HIS 0.004 0.001 HIS A 712 PHE 0.010 0.001 PHE A 674 TYR 0.011 0.001 TYR A 882 ARG 0.003 0.000 ARG A 621 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3015.66 seconds wall clock time: 54 minutes 58.35 seconds (3298.35 seconds total)