Starting phenix.real_space_refine on Thu Feb 15 13:45:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx9_23063/02_2024/7kx9_23063_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx9_23063/02_2024/7kx9_23063.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx9_23063/02_2024/7kx9_23063_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx9_23063/02_2024/7kx9_23063_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx9_23063/02_2024/7kx9_23063_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx9_23063/02_2024/7kx9_23063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx9_23063/02_2024/7kx9_23063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx9_23063/02_2024/7kx9_23063_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx9_23063/02_2024/7kx9_23063_trim_updated.pdb" } resolution = 3.5 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= 0.003 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 25 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 40 5.49 5 Mg 2 5.21 5 S 33 5.16 5 C 4015 2.51 5 N 1170 2.21 5 O 1318 1.98 5 H 5832 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A ARG 269": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 330": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 342": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 351": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 354": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 382": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 434": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 452": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 471": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 481": "OE1" <-> "OE2" Residue "A ARG 488": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 539": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 550": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 555": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A ARG 576": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 584": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A ASP 604": "OD1" <-> "OD2" Residue "A ARG 607": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 608": "OE1" <-> "OE2" Residue "A ARG 629": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 665": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 671": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 674": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A ARG 680": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 692": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 695": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 717": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 726": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 789": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 798": "OE1" <-> "OE2" Residue "A ARG 836": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 838": "OE1" <-> "OE2" Residue "A GLU 844": "OE1" <-> "OE2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A ARG 871": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 875": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 879": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 911": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 921": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 966": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 974": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 983": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12410 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 11133 Classifications: {'peptide': 734} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 38, 'TRANS': 695} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 760 Classifications: {'RNA': 24} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p': 1, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 515 Classifications: {'RNA': 16} Modifications used: {'3*END': 1, 'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.10, per 1000 atoms: 0.49 Number of scatterers: 12410 At special positions: 0 Unit cell: (79.35, 109.25, 75.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 33 16.00 P 40 15.00 Mg 2 11.99 O 1318 8.00 N 1170 7.00 C 4015 6.00 H 5832 1.00 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 - 3.50 Amino acid : False - 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: 10.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 13 sheets defined 29.6% alpha, 14.9% beta 10 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 6.79 Creating SS restraints... Processing helix chain 'A' and resid 268 through 278 removed outlier: 3.644A pdb=" N GLU A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N HIS A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 346 removed outlier: 3.708A pdb=" N ARG A 345 " --> pdb=" O LYS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 465 through 473 Processing helix chain 'A' and resid 522 through 526 Processing helix chain 'A' and resid 529 through 538 removed outlier: 3.641A pdb=" N VAL A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N HIS A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 557 Processing helix chain 'A' and resid 560 through 569 Processing helix chain 'A' and resid 606 through 611 removed outlier: 3.738A pdb=" N LYS A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 645 removed outlier: 5.109A pdb=" N GLY A 633 " --> pdb=" O LYS A 630 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 634 " --> pdb=" O ASP A 631 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP A 637 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 640 " --> pdb=" O ASP A 637 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 645 " --> pdb=" O LEU A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 666 through 676 Processing helix chain 'A' and resid 693 through 704 Processing helix chain 'A' and resid 725 through 740 removed outlier: 3.560A pdb=" N LEU A 734 " --> pdb=" O GLN A 730 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 740 " --> pdb=" O MET A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 818 Processing helix chain 'A' and resid 837 through 850 removed outlier: 4.190A pdb=" N SER A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Proline residue: A 846 - end of helix Processing helix chain 'A' and resid 853 through 855 No H-bonds generated for 'chain 'A' and resid 853 through 855' Processing helix chain 'A' and resid 931 through 943 removed outlier: 3.691A pdb=" N THR A 942 " --> pdb=" O THR A 938 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N HIS A 943 " --> pdb=" O TYR A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 968 Processing sheet with id= A, first strand: chain 'A' and resid 236 through 242 removed outlier: 3.804A pdb=" N LEU A 578 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 245 through 247 removed outlier: 4.439A pdb=" N LEU A 387 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 390 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 379 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 392 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP A 373 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 257 through 261 removed outlier: 3.567A pdb=" N SER A 322 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 307 through 309 Processing sheet with id= E, first strand: chain 'A' and resid 350 through 352 removed outlier: 3.556A pdb=" N TYR A 357 " --> pdb=" O GLN A 350 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 431 through 433 removed outlier: 3.512A pdb=" N ARG A 438 " --> pdb=" O THR A 433 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 444 through 446 removed outlier: 3.519A pdb=" N ALA A 446 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 484 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 454 through 456 Processing sheet with id= I, first strand: chain 'A' and resid 589 through 591 Processing sheet with id= J, first strand: chain 'A' and resid 624 through 626 removed outlier: 3.519A pdb=" N PHE A 688 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 775 through 777 removed outlier: 6.291A pdb=" N ARG A 824 " --> pdb=" O MET A 755 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL A 757 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE A 826 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ILE A 759 " --> pdb=" O ILE A 826 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE A 828 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LYS A 862 " --> pdb=" O ILE A 825 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL A 827 " --> pdb=" O LYS A 862 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ALA A 864 " --> pdb=" O VAL A 827 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 867 through 869 Processing sheet with id= M, first strand: chain 'A' and resid 878 through 880 180 hydrogen bonds defined for protein. 477 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 4.45 Time building geometry restraints manager: 10.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5820 1.03 - 1.23: 40 1.23 - 1.42: 2910 1.42 - 1.61: 3808 1.61 - 1.81: 54 Bond restraints: 12632 Sorted by residual: bond pdb=" C6 OMG B 24 " pdb=" O6 OMG B 24 " ideal model delta sigma weight residual 1.239 1.168 0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" P OMG B 24 " pdb=" OP1 OMG B 24 " ideal model delta sigma weight residual 1.439 1.504 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C2 OMG B 24 " pdb=" N2 OMG B 24 " ideal model delta sigma weight residual 1.433 1.487 -0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" N ARG A 269 " pdb=" H ARG A 269 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.52e+00 bond pdb=" C PHE A 877 " pdb=" N GLY A 878 " ideal model delta sigma weight residual 1.331 1.317 0.014 6.60e-03 2.30e+04 4.51e+00 ... (remaining 12627 not shown) Histogram of bond angle deviations from ideal: 80.60 - 94.80: 2 94.80 - 109.00: 6158 109.00 - 123.20: 15270 123.20 - 137.40: 1244 137.40 - 151.60: 1 Bond angle restraints: 22675 Sorted by residual: angle pdb=" C1' OMG B 24 " pdb=" N9 OMG B 24 " pdb=" C4 OMG B 24 " ideal model delta sigma weight residual 108.29 151.60 -43.31 3.00e+00 1.11e-01 2.08e+02 angle pdb=" C1' OMG B 24 " pdb=" N9 OMG B 24 " pdb=" C8 OMG B 24 " ideal model delta sigma weight residual 142.82 100.49 42.33 3.00e+00 1.11e-01 1.99e+02 angle pdb=" O3' U B 10 " pdb=" P U B 11 " pdb=" OP1 U B 11 " ideal model delta sigma weight residual 108.00 80.60 27.40 3.00e+00 1.11e-01 8.34e+01 angle pdb=" O3' U B 10 " pdb=" P U B 11 " pdb=" OP2 U B 11 " ideal model delta sigma weight residual 108.00 83.25 24.75 3.00e+00 1.11e-01 6.80e+01 angle pdb=" OP1 U B 11 " pdb=" P U B 11 " pdb=" OP2 U B 11 " ideal model delta sigma weight residual 119.60 130.39 -10.79 3.00e+00 1.11e-01 1.29e+01 ... (remaining 22670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.09: 5571 24.09 - 48.19: 334 48.19 - 72.28: 89 72.28 - 96.37: 19 96.37 - 120.47: 4 Dihedral angle restraints: 6017 sinusoidal: 3512 harmonic: 2505 Sorted by residual: dihedral pdb=" CA ARG A 286 " pdb=" C ARG A 286 " pdb=" N VAL A 287 " pdb=" CA VAL A 287 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA SER A 850 " pdb=" C SER A 850 " pdb=" N CYS A 851 " pdb=" CA CYS A 851 " ideal model delta harmonic sigma weight residual -180.00 -159.83 -20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA HIS A 895 " pdb=" C HIS A 895 " pdb=" N THR A 896 " pdb=" CA THR A 896 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 6014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.384: 1084 0.384 - 0.768: 0 0.768 - 1.152: 0 1.152 - 1.536: 0 1.536 - 1.921: 1 Chirality restraints: 1085 Sorted by residual: chirality pdb=" P U B 11 " pdb=" OP1 U B 11 " pdb=" OP2 U B 11 " pdb=" O5' U B 11 " both_signs ideal model delta sigma weight residual True 2.41 0.49 1.92 2.00e-01 2.50e+01 9.22e+01 chirality pdb=" C1' G C 22 " pdb=" O4' G C 22 " pdb=" C2' G C 22 " pdb=" N9 G C 22 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CA MET A 398 " pdb=" N MET A 398 " pdb=" C MET A 398 " pdb=" CB MET A 398 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 1082 not shown) Planarity restraints: 1719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG B 24 " 0.004 2.00e-02 2.50e+03 4.71e-01 4.99e+03 pdb=" C4' OMG B 24 " -0.406 2.00e-02 2.50e+03 pdb=" O4' OMG B 24 " -0.450 2.00e-02 2.50e+03 pdb=" C3' OMG B 24 " 0.562 2.00e-02 2.50e+03 pdb=" O3' OMG B 24 " 0.388 2.00e-02 2.50e+03 pdb=" C2' OMG B 24 " 0.267 2.00e-02 2.50e+03 pdb=" O2' OMG B 24 " -0.764 2.00e-02 2.50e+03 pdb=" C1' OMG B 24 " -0.264 2.00e-02 2.50e+03 pdb=" N9 OMG B 24 " 0.662 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 860 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO A 861 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 861 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 861 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 397 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C VAL A 397 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 397 " -0.010 2.00e-02 2.50e+03 pdb=" N MET A 398 " -0.009 2.00e-02 2.50e+03 ... (remaining 1716 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.86: 53 1.86 - 2.54: 10720 2.54 - 3.23: 36589 3.23 - 3.91: 45751 3.91 - 4.60: 73660 Nonbonded interactions: 166773 Sorted by model distance: nonbonded pdb="HH21 ARG A 953 " pdb=" OP2 U B 6 " model vdw 1.172 1.850 nonbonded pdb=" HD1 HIS A 962 " pdb="MG MG A1002 " model vdw 1.466 1.700 nonbonded pdb="HE22 GLN A 735 " pdb="MG MG A1001 " model vdw 1.547 1.700 nonbonded pdb=" O ASN A 663 " pdb=" HG SER A 668 " model vdw 1.548 1.850 nonbonded pdb=" OD2 ASP A 527 " pdb=" H VAL A 530 " model vdw 1.611 1.850 ... (remaining 166768 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.190 Extract box with map and model: 0.860 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 46.860 Find NCS groups from input model: 0.220 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 : 0.007 0.071 6800 Z= 0.448 Angle : 1.029 43.312 9412 Z= 0.475 Chirality : 0.074 1.921 1085 Planarity : 0.015 0.471 1063 Dihedral : 17.341 120.468 2757 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 0.17 % Allowed : 0.17 % Favored : 99.67 % 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: -3.70 (0.30), residues: 728 helix: -0.96 (0.34), residues: 224 sheet: -3.45 (0.34), residues: 187 loop : -2.83 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 623 HIS 0.009 0.001 HIS A 487 PHE 0.009 0.001 PHE A 340 TYR 0.011 0.002 TYR A 435 ARG 0.010 0.001 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 LEU cc_start: 0.8702 (mt) cc_final: 0.8457 (mt) REVERT: A 908 GLN cc_start: 0.7761 (tp40) cc_final: 0.7422 (tp40) outliers start: 1 outliers final: 1 residues processed: 85 average time/residue: 0.4253 time to fit residues: 47.0302 Evaluate side-chains 68 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 882 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6800 Z= 0.356 Angle : 0.829 27.586 9412 Z= 0.418 Chirality : 0.072 1.880 1085 Planarity : 0.006 0.112 1063 Dihedral : 18.666 132.807 1412 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 0.33 % Allowed : 5.17 % Favored : 94.50 % 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: -3.22 (0.30), residues: 728 helix: -0.51 (0.34), residues: 217 sheet: -2.84 (0.37), residues: 174 loop : -2.83 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 594 PHE 0.018 0.001 PHE A 340 TYR 0.013 0.001 TYR A 376 ARG 0.006 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ILE cc_start: 0.9234 (pt) cc_final: 0.8974 (mt) REVERT: A 398 MET cc_start: 0.7160 (mmp) cc_final: 0.6658 (mmp) REVERT: A 621 LEU cc_start: 0.8645 (mt) cc_final: 0.8439 (mt) REVERT: A 793 GLN cc_start: 0.6662 (mp10) cc_final: 0.4366 (mp10) REVERT: A 908 GLN cc_start: 0.7682 (tp40) cc_final: 0.7432 (tp40) outliers start: 2 outliers final: 1 residues processed: 76 average time/residue: 0.3639 time to fit residues: 37.7060 Evaluate side-chains 71 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 771 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6800 Z= 0.236 Angle : 0.761 26.918 9412 Z= 0.385 Chirality : 0.072 1.922 1085 Planarity : 0.005 0.113 1063 Dihedral : 18.379 123.423 1410 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.67 % Allowed : 6.50 % Favored : 92.83 % 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: -2.80 (0.31), residues: 728 helix: -0.05 (0.36), residues: 216 sheet: -2.60 (0.37), residues: 178 loop : -2.64 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.010 0.001 HIS A 763 PHE 0.014 0.001 PHE A 340 TYR 0.011 0.001 TYR A 435 ARG 0.003 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 339 ILE cc_start: 0.9265 (pt) cc_final: 0.8989 (mt) REVERT: A 793 GLN cc_start: 0.6198 (mp10) cc_final: 0.4401 (mp10) REVERT: A 801 HIS cc_start: 0.8298 (t70) cc_final: 0.8031 (t-170) REVERT: A 871 ARG cc_start: 0.8070 (mtm110) cc_final: 0.7870 (mtp-110) REVERT: A 908 GLN cc_start: 0.7622 (tp40) cc_final: 0.7389 (tp40) outliers start: 4 outliers final: 3 residues processed: 78 average time/residue: 0.4086 time to fit residues: 42.6441 Evaluate side-chains 70 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 830 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6800 Z= 0.300 Angle : 0.766 27.059 9412 Z= 0.387 Chirality : 0.072 1.913 1085 Planarity : 0.006 0.112 1063 Dihedral : 18.288 125.039 1410 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 0.67 % Allowed : 8.50 % Favored : 90.83 % 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: -2.62 (0.31), residues: 728 helix: 0.08 (0.36), residues: 216 sheet: -2.54 (0.37), residues: 173 loop : -2.50 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 763 PHE 0.017 0.001 PHE A 340 TYR 0.009 0.001 TYR A 376 ARG 0.004 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.894 Fit side-chains REVERT: A 339 ILE cc_start: 0.9250 (pt) cc_final: 0.9017 (mt) REVERT: A 801 HIS cc_start: 0.8327 (t70) cc_final: 0.8094 (t-170) outliers start: 4 outliers final: 3 residues processed: 74 average time/residue: 0.4037 time to fit residues: 39.7627 Evaluate side-chains 71 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 771 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 594 HIS ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6800 Z= 0.255 Angle : 0.747 26.968 9412 Z= 0.379 Chirality : 0.072 1.925 1085 Planarity : 0.005 0.112 1063 Dihedral : 18.208 126.846 1410 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.17 % Allowed : 9.50 % Favored : 89.33 % 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: -2.41 (0.31), residues: 728 helix: 0.25 (0.36), residues: 217 sheet: -2.34 (0.38), residues: 173 loop : -2.42 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 594 PHE 0.014 0.001 PHE A 340 TYR 0.011 0.001 TYR A 435 ARG 0.003 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.938 Fit side-chains REVERT: A 339 ILE cc_start: 0.9227 (pt) cc_final: 0.9010 (mt) REVERT: A 641 MET cc_start: 0.8509 (tpp) cc_final: 0.8035 (mmt) REVERT: A 793 GLN cc_start: 0.6546 (mp10) cc_final: 0.5660 (mt0) REVERT: A 802 GLU cc_start: 0.6075 (mt-10) cc_final: 0.5835 (mt-10) outliers start: 7 outliers final: 6 residues processed: 76 average time/residue: 0.4462 time to fit residues: 45.1002 Evaluate side-chains 75 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 830 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 14 optimal weight: 0.0370 chunk 43 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 0.0370 chunk 38 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 overall best weight: 1.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6800 Z= 0.149 Angle : 0.721 26.802 9412 Z= 0.364 Chirality : 0.072 1.951 1085 Planarity : 0.005 0.112 1063 Dihedral : 18.066 127.705 1410 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.83 % Allowed : 10.50 % Favored : 88.67 % 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: -2.10 (0.32), residues: 728 helix: 0.52 (0.36), residues: 224 sheet: -2.20 (0.39), residues: 171 loop : -2.28 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.009 0.001 HIS A 801 PHE 0.009 0.001 PHE A 340 TYR 0.007 0.001 TYR A 376 ARG 0.004 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ILE cc_start: 0.9242 (pt) cc_final: 0.8980 (mt) outliers start: 5 outliers final: 4 residues processed: 78 average time/residue: 0.4633 time to fit residues: 48.1880 Evaluate side-chains 73 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 564 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 50.0000 chunk 41 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 40.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6800 Z= 0.321 Angle : 0.757 27.118 9412 Z= 0.382 Chirality : 0.072 1.929 1085 Planarity : 0.005 0.112 1063 Dihedral : 18.108 130.253 1410 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 1.33 % Allowed : 11.00 % Favored : 87.67 % 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: -2.18 (0.32), residues: 728 helix: 0.45 (0.36), residues: 223 sheet: -2.20 (0.39), residues: 173 loop : -2.35 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 605 HIS 0.005 0.001 HIS A 763 PHE 0.017 0.001 PHE A 340 TYR 0.011 0.001 TYR A 435 ARG 0.003 0.000 ARG A 879 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 ILE cc_start: 0.9267 (pt) cc_final: 0.8973 (mt) REVERT: A 398 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.6930 (mmt) outliers start: 8 outliers final: 7 residues processed: 74 average time/residue: 0.4076 time to fit residues: 40.0887 Evaluate side-chains 71 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 830 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 57 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6800 Z= 0.166 Angle : 0.726 26.829 9412 Z= 0.367 Chirality : 0.072 1.953 1085 Planarity : 0.005 0.112 1063 Dihedral : 18.007 131.723 1410 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.00 % Allowed : 11.50 % Favored : 87.50 % 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: -1.89 (0.32), residues: 728 helix: 0.75 (0.37), residues: 224 sheet: -2.04 (0.39), residues: 173 loop : -2.22 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.004 0.001 HIS A 801 PHE 0.013 0.001 PHE A 406 TYR 0.009 0.001 TYR A 435 ARG 0.003 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ILE cc_start: 0.9243 (pt) cc_final: 0.8942 (mt) outliers start: 6 outliers final: 6 residues processed: 72 average time/residue: 0.4330 time to fit residues: 41.4238 Evaluate side-chains 72 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 771 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6800 Z= 0.348 Angle : 0.758 27.137 9412 Z= 0.384 Chirality : 0.072 1.929 1085 Planarity : 0.005 0.112 1063 Dihedral : 18.075 134.298 1410 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 1.33 % Allowed : 11.33 % Favored : 87.33 % 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: -2.05 (0.32), residues: 728 helix: 0.64 (0.36), residues: 224 sheet: -2.14 (0.39), residues: 174 loop : -2.34 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 605 HIS 0.005 0.001 HIS A 801 PHE 0.019 0.001 PHE A 340 TYR 0.010 0.001 TYR A 356 ARG 0.003 0.000 ARG A 879 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ILE cc_start: 0.9274 (pt) cc_final: 0.8964 (mt) REVERT: A 398 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.6959 (mmt) REVERT: A 641 MET cc_start: 0.8554 (mmt) cc_final: 0.8095 (mmt) outliers start: 8 outliers final: 7 residues processed: 70 average time/residue: 0.4516 time to fit residues: 42.2571 Evaluate side-chains 71 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 771 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 8 optimal weight: 30.0000 chunk 16 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6800 Z= 0.210 Angle : 0.733 26.947 9412 Z= 0.370 Chirality : 0.071 1.943 1085 Planarity : 0.005 0.112 1063 Dihedral : 18.004 135.656 1410 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.00 % Allowed : 11.67 % Favored : 87.33 % 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: -1.86 (0.32), residues: 728 helix: 0.83 (0.37), residues: 224 sheet: -2.02 (0.39), residues: 174 loop : -2.26 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.005 0.001 HIS A 801 PHE 0.015 0.001 PHE A 406 TYR 0.007 0.001 TYR A 376 ARG 0.003 0.000 ARG A 396 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ILE cc_start: 0.9249 (pt) cc_final: 0.8926 (mt) REVERT: A 398 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6830 (mmt) REVERT: A 641 MET cc_start: 0.8527 (mmt) cc_final: 0.8069 (mmt) outliers start: 6 outliers final: 5 residues processed: 69 average time/residue: 0.4598 time to fit residues: 42.1401 Evaluate side-chains 71 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 564 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 11 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.146156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.102035 restraints weight = 26268.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108205 restraints weight = 12419.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112089 restraints weight = 8176.872| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6800 Z= 0.217 Angle : 0.727 26.938 9412 Z= 0.367 Chirality : 0.072 1.952 1085 Planarity : 0.005 0.112 1063 Dihedral : 17.925 138.528 1410 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 1.00 % Allowed : 11.67 % Favored : 87.33 % 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: -1.72 (0.33), residues: 728 helix: 0.96 (0.37), residues: 224 sheet: -1.95 (0.40), residues: 173 loop : -2.17 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 605 HIS 0.005 0.001 HIS A 801 PHE 0.012 0.001 PHE A 340 TYR 0.008 0.001 TYR A 356 ARG 0.002 0.000 ARG A 396 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2952.35 seconds wall clock time: 53 minutes 19.87 seconds (3199.87 seconds total)