Starting phenix.real_space_refine on Tue Feb 13 11:52:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx7_23061/02_2024/7kx7_23061_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx7_23061/02_2024/7kx7_23061.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx7_23061/02_2024/7kx7_23061_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx7_23061/02_2024/7kx7_23061_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx7_23061/02_2024/7kx7_23061_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx7_23061/02_2024/7kx7_23061.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx7_23061/02_2024/7kx7_23061.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx7_23061/02_2024/7kx7_23061_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx7_23061/02_2024/7kx7_23061_updated.pdb" } resolution = 3.8 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= 0.028 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 82 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 2 5.21 5 S 33 5.16 5 C 3676 2.51 5 N 1035 2.21 5 O 1075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 382": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A ARG 434": "NH1" <-> "NH2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A ASP 474": "OD1" <-> "OD2" Residue "A ASP 476": "OD1" <-> "OD2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "A ARG 539": "NH1" <-> "NH2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A GLU 588": "OE1" <-> "OE2" Residue "A ASP 604": "OD1" <-> "OD2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A ARG 629": "NH1" <-> "NH2" Residue "A ARG 665": "NH1" <-> "NH2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ARG 674": "NH1" <-> "NH2" Residue "A ARG 680": "NH1" <-> "NH2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A ARG 695": "NH1" <-> "NH2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A ARG 726": "NH1" <-> "NH2" Residue "A PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A GLU 802": "OE1" <-> "OE2" Residue "A TYR 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ARG 871": "NH1" <-> "NH2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A ARG 879": "NH1" <-> "NH2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 911": "NH1" <-> "NH2" Residue "A ARG 921": "NH1" <-> "NH2" Residue "A ARG 974": "NH1" <-> "NH2" Residue "A GLU 979": "OE1" <-> "OE2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A PHE 986": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 5828 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5679 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 38, 'TRANS': 690} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 106 Chain: "B" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Classifications: {'RNA': 7} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p': 1, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 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: 4.16, per 1000 atoms: 0.71 Number of scatterers: 5828 At special positions: 0 Unit cell: (78.2, 103.5, 79.35, 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) S 33 16.00 P 7 15.00 Mg 2 11.99 O 1075 8.00 N 1035 7.00 C 3676 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 - 3.50 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: 2.97 Conformation dependent library (CDL) restraints added in 1.4 seconds 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 11 sheets defined 28.5% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 268 through 281 removed outlier: 4.030A pdb=" N GLU A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N HIS A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLU A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 346 removed outlier: 3.653A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 465 through 473 Processing helix chain 'A' and resid 529 through 538 removed outlier: 3.826A pdb=" N ASP A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N HIS A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 556 removed outlier: 3.646A pdb=" N GLU A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 569 removed outlier: 3.691A pdb=" N LEU A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 610 No H-bonds generated for 'chain 'A' and resid 608 through 610' Processing helix chain 'A' and resid 629 through 649 removed outlier: 5.501A pdb=" N GLY A 633 " --> pdb=" O LYS A 630 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 634 " --> pdb=" O ASP A 631 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 643 " --> pdb=" O ASN A 640 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N CYS A 646 " --> pdb=" O SER A 643 " (cutoff:3.500A) Proline residue: A 647 - end of helix Processing helix chain 'A' and resid 666 through 674 Processing helix chain 'A' and resid 693 through 704 removed outlier: 3.835A pdb=" N LEU A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 718 No H-bonds generated for 'chain 'A' and resid 716 through 718' Processing helix chain 'A' and resid 726 through 740 removed outlier: 3.805A pdb=" N LEU A 734 " --> pdb=" O GLN A 730 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 735 " --> pdb=" O LYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 818 removed outlier: 4.601A pdb=" N LYS A 804 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 805 " --> pdb=" O HIS A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 854 removed outlier: 5.836A pdb=" N VAL A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Proline residue: A 846 - end of helix removed outlier: 3.828A pdb=" N PHE A 852 " --> pdb=" O PHE A 848 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N SER A 853 " --> pdb=" O ASN A 849 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE A 854 " --> pdb=" O SER A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 944 removed outlier: 3.917A pdb=" N THR A 942 " --> pdb=" O THR A 938 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N HIS A 943 " --> pdb=" O TYR A 939 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 970 Processing helix chain 'A' and resid 978 through 980 No H-bonds generated for 'chain 'A' and resid 978 through 980' Processing sheet with id= A, first strand: chain 'A' and resid 580 through 583 removed outlier: 3.671A pdb=" N VAL A 240 " --> pdb=" O MET A 580 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 244 through 247 removed outlier: 4.781A pdb=" N LEU A 387 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 388 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN A 381 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 372 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 256 through 258 Processing sheet with id= D, first strand: chain 'A' and resid 306 through 308 Processing sheet with id= E, first strand: chain 'A' and resid 350 through 352 removed outlier: 3.616A pdb=" N ASP A 355 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 431 through 433 Processing sheet with id= G, first strand: chain 'A' and resid 454 through 457 removed outlier: 3.548A pdb=" N ILE A 463 " --> pdb=" O PHE A 455 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 485 through 487 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 657 through 660 removed outlier: 3.600A pdb=" N VAL A 625 " --> pdb=" O LYS A 657 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 627 " --> pdb=" O VAL A 659 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 786 through 791 removed outlier: 3.605A pdb=" N ALA A 773 " --> pdb=" O ALA A 791 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 772 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP A 760 " --> pdb=" O GLY A 774 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL A 756 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ARG A 824 " --> pdb=" O MET A 755 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL A 757 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE A 826 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE A 759 " --> pdb=" O ILE A 826 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE A 828 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N VAL A 761 " --> pdb=" O PHE A 828 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS A 862 " --> pdb=" O ILE A 825 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL A 827 " --> pdb=" O LYS A 862 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA A 864 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG A 829 " --> pdb=" O ALA A 864 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N VAL A 866 " --> pdb=" O ARG A 829 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL A 867 " --> pdb=" O VAL A 922 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL A 922 " --> pdb=" O VAL A 867 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLN A 869 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR A 920 " --> pdb=" O GLN A 869 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 891 " --> pdb=" O VAL A 906 " (cutoff:3.500A) 171 hydrogen bonds defined for protein. 453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 937 1.32 - 1.44: 1594 1.44 - 1.57: 3365 1.57 - 1.69: 12 1.69 - 1.82: 54 Bond restraints: 5962 Sorted by residual: bond pdb=" N ASP A 902 " pdb=" CA ASP A 902 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.29e-02 6.01e+03 7.18e+00 bond pdb=" N LYS A 899 " pdb=" CA LYS A 899 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.29e-02 6.01e+03 6.74e+00 bond pdb=" N PHE A 903 " pdb=" CA PHE A 903 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.29e-02 6.01e+03 6.72e+00 bond pdb=" N TYR A 904 " pdb=" CA TYR A 904 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.22e-02 6.72e+03 6.68e+00 bond pdb=" N ILE A 719 " pdb=" CA ILE A 719 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.62e+00 ... (remaining 5957 not shown) Histogram of bond angle deviations from ideal: 98.78 - 105.84: 172 105.84 - 112.89: 3250 112.89 - 119.95: 2010 119.95 - 127.00: 2601 127.00 - 134.06: 79 Bond angle restraints: 8112 Sorted by residual: angle pdb=" N GLN A 721 " pdb=" CA GLN A 721 " pdb=" C GLN A 721 " ideal model delta sigma weight residual 113.23 108.30 4.93 1.22e+00 6.72e-01 1.63e+01 angle pdb=" CA LYS A 899 " pdb=" C LYS A 899 " pdb=" O LYS A 899 " ideal model delta sigma weight residual 121.44 117.00 4.44 1.17e+00 7.31e-01 1.44e+01 angle pdb=" CA ILE A 299 " pdb=" C ILE A 299 " pdb=" O ILE A 299 " ideal model delta sigma weight residual 122.13 118.05 4.08 1.11e+00 8.12e-01 1.35e+01 angle pdb=" N GLN A 722 " pdb=" CA GLN A 722 " pdb=" C GLN A 722 " ideal model delta sigma weight residual 112.72 108.37 4.35 1.28e+00 6.10e-01 1.16e+01 angle pdb=" CA ASP A 902 " pdb=" C ASP A 902 " pdb=" O ASP A 902 " ideal model delta sigma weight residual 121.44 117.52 3.92 1.17e+00 7.31e-01 1.12e+01 ... (remaining 8107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 3278 17.39 - 34.78: 288 34.78 - 52.16: 38 52.16 - 69.55: 14 69.55 - 86.94: 11 Dihedral angle restraints: 3629 sinusoidal: 1487 harmonic: 2142 Sorted by residual: dihedral pdb=" CA ASN A 262 " pdb=" C ASN A 262 " pdb=" N PRO A 263 " pdb=" CA PRO A 263 " ideal model delta harmonic sigma weight residual 180.00 154.70 25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ASP A 325 " pdb=" C ASP A 325 " pdb=" N SER A 326 " pdb=" CA SER A 326 " ideal model delta harmonic sigma weight residual 180.00 157.10 22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA PRO A 512 " pdb=" C PRO A 512 " pdb=" N GLU A 513 " pdb=" CA GLU A 513 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 3626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 710 0.058 - 0.116: 182 0.116 - 0.174: 17 0.174 - 0.232: 5 0.232 - 0.290: 3 Chirality restraints: 917 Sorted by residual: chirality pdb=" CA ILE A 897 " pdb=" N ILE A 897 " pdb=" C ILE A 897 " pdb=" CB ILE A 897 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA ILE A 719 " pdb=" N ILE A 719 " pdb=" C ILE A 719 " pdb=" CB ILE A 719 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ASN A 262 " pdb=" N ASN A 262 " pdb=" C ASN A 262 " pdb=" CB ASN A 262 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 914 not shown) Planarity restraints: 1019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC B 25 " -0.015 2.00e-02 2.50e+03 5.14e-01 5.94e+03 pdb=" C4' OMC B 25 " -0.413 2.00e-02 2.50e+03 pdb=" O4' OMC B 25 " -0.514 2.00e-02 2.50e+03 pdb=" C3' OMC B 25 " 0.574 2.00e-02 2.50e+03 pdb=" O3' OMC B 25 " 0.474 2.00e-02 2.50e+03 pdb=" C2' OMC B 25 " 0.234 2.00e-02 2.50e+03 pdb=" O2' OMC B 25 " -0.838 2.00e-02 2.50e+03 pdb=" C1' OMC B 25 " -0.255 2.00e-02 2.50e+03 pdb=" N1 OMC B 25 " 0.752 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 522 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C ASP A 522 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP A 522 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA A 523 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 647 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 648 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 648 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 648 " -0.028 5.00e-02 4.00e+02 ... (remaining 1016 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 63 2.54 - 3.13: 4725 3.13 - 3.72: 8816 3.72 - 4.31: 11939 4.31 - 4.90: 20319 Nonbonded interactions: 45862 Sorted by model distance: nonbonded pdb=" OP1 U B 3 " pdb="MG MG A1001 " model vdw 1.953 2.170 nonbonded pdb=" OXT LEU A 987 " pdb="MG MG A1001 " model vdw 1.963 2.170 nonbonded pdb=" O LEU A 987 " pdb="MG MG A1001 " model vdw 1.997 2.170 nonbonded pdb=" NH2 ARG A 583 " pdb=" OE1 GLN A 935 " model vdw 2.201 2.520 nonbonded pdb=" OE1 GLU A 364 " pdb=" NE2 GLN A 371 " model vdw 2.221 2.520 ... (remaining 45857 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: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.440 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.006 0.050 5962 Z= 0.422 Angle : 0.775 6.509 8112 Z= 0.462 Chirality : 0.053 0.290 917 Planarity : 0.017 0.514 1019 Dihedral : 14.039 86.937 2241 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.17 % Allowed : 0.67 % Favored : 99.16 % 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: -2.63 (0.31), residues: 721 helix: -0.03 (0.38), residues: 199 sheet: -2.35 (0.41), residues: 147 loop : -2.50 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 373 HIS 0.006 0.001 HIS A 909 PHE 0.013 0.002 PHE A 852 TYR 0.032 0.002 TYR A 859 ARG 0.008 0.001 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 517 MET cc_start: 0.7805 (mpp) cc_final: 0.7497 (mpp) REVERT: A 743 GLU cc_start: 0.8404 (pm20) cc_final: 0.7992 (pt0) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.2088 time to fit residues: 23.8838 Evaluate side-chains 68 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 0.0040 chunk 36 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 overall best weight: 4.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 GLN ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN A 959 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5962 Z= 0.271 Angle : 0.707 14.506 8112 Z= 0.391 Chirality : 0.045 0.197 917 Planarity : 0.006 0.118 1019 Dihedral : 9.136 73.672 904 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.68 % Allowed : 9.23 % Favored : 89.09 % 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: -2.37 (0.31), residues: 721 helix: 0.39 (0.39), residues: 193 sheet: -2.12 (0.40), residues: 144 loop : -2.46 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 373 HIS 0.005 0.001 HIS A 909 PHE 0.028 0.002 PHE A 528 TYR 0.021 0.002 TYR A 859 ARG 0.003 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.727 Fit side-chains REVERT: A 517 MET cc_start: 0.7742 (mpp) cc_final: 0.7510 (mpp) REVERT: A 658 MET cc_start: 0.8563 (tpp) cc_final: 0.8344 (tpp) REVERT: A 902 ASP cc_start: 0.7593 (p0) cc_final: 0.7300 (p0) outliers start: 10 outliers final: 7 residues processed: 79 average time/residue: 0.1705 time to fit residues: 18.4060 Evaluate side-chains 70 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 680 ARG Chi-restraints excluded: chain A residue 693 ASP Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 959 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 18 optimal weight: 0.0070 chunk 65 optimal weight: 0.2980 chunk 70 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 overall best weight: 4.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5962 Z= 0.263 Angle : 0.654 13.898 8112 Z= 0.370 Chirality : 0.044 0.181 917 Planarity : 0.005 0.116 1019 Dihedral : 9.110 73.690 904 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 2.52 % Allowed : 11.91 % Favored : 85.57 % 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: -2.24 (0.31), residues: 721 helix: 0.41 (0.39), residues: 199 sheet: -2.07 (0.40), residues: 144 loop : -2.36 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 623 HIS 0.004 0.001 HIS A 909 PHE 0.028 0.002 PHE A 528 TYR 0.019 0.001 TYR A 859 ARG 0.003 0.000 ARG A 665 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 0.682 Fit side-chains REVERT: A 465 PHE cc_start: 0.8648 (m-80) cc_final: 0.8312 (m-80) REVERT: A 573 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8057 (mp) REVERT: A 902 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7218 (p0) outliers start: 15 outliers final: 8 residues processed: 75 average time/residue: 0.1698 time to fit residues: 17.4128 Evaluate side-chains 77 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 680 ARG Chi-restraints excluded: chain A residue 693 ASP Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 902 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 0.0470 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 18 optimal weight: 30.0000 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5962 Z= 0.224 Angle : 0.639 13.384 8112 Z= 0.362 Chirality : 0.044 0.175 917 Planarity : 0.005 0.115 1019 Dihedral : 9.165 73.625 904 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.35 % Allowed : 13.26 % Favored : 84.40 % 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: -2.10 (0.32), residues: 721 helix: 0.55 (0.40), residues: 200 sheet: -2.03 (0.40), residues: 143 loop : -2.27 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 623 HIS 0.004 0.001 HIS A 909 PHE 0.020 0.002 PHE A 852 TYR 0.021 0.001 TYR A 859 ARG 0.004 0.000 ARG A 665 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.749 Fit side-chains REVERT: A 465 PHE cc_start: 0.8614 (m-80) cc_final: 0.8253 (m-80) REVERT: A 902 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7136 (p0) outliers start: 14 outliers final: 7 residues processed: 78 average time/residue: 0.1695 time to fit residues: 18.1109 Evaluate side-chains 80 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 693 ASP Chi-restraints excluded: chain A residue 902 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 0.0970 chunk 48 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 17 optimal weight: 30.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5962 Z= 0.222 Angle : 0.639 13.163 8112 Z= 0.359 Chirality : 0.043 0.169 917 Planarity : 0.005 0.115 1019 Dihedral : 9.211 73.630 904 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.35 % Allowed : 14.60 % Favored : 83.05 % 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: -2.00 (0.32), residues: 721 helix: 0.66 (0.40), residues: 200 sheet: -2.03 (0.40), residues: 143 loop : -2.21 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 623 HIS 0.003 0.001 HIS A 909 PHE 0.014 0.002 PHE A 406 TYR 0.018 0.001 TYR A 859 ARG 0.004 0.000 ARG A 665 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.721 Fit side-chains REVERT: A 465 PHE cc_start: 0.8591 (m-80) cc_final: 0.8177 (m-80) REVERT: A 902 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7105 (p0) outliers start: 14 outliers final: 12 residues processed: 83 average time/residue: 0.1608 time to fit residues: 18.4205 Evaluate side-chains 86 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 693 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 902 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 5962 Z= 0.433 Angle : 0.724 14.149 8112 Z= 0.397 Chirality : 0.046 0.200 917 Planarity : 0.006 0.115 1019 Dihedral : 9.536 73.928 904 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 3.52 % Allowed : 14.93 % Favored : 81.54 % 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: -2.17 (0.31), residues: 721 helix: 0.52 (0.40), residues: 198 sheet: -1.92 (0.41), residues: 141 loop : -2.39 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 623 HIS 0.007 0.001 HIS A 368 PHE 0.030 0.002 PHE A 852 TYR 0.019 0.002 TYR A 859 ARG 0.004 0.000 ARG A 665 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 71 time to evaluate : 0.702 Fit side-chains REVERT: A 465 PHE cc_start: 0.8648 (m-80) cc_final: 0.8241 (m-80) REVERT: A 605 TRP cc_start: 0.8916 (p90) cc_final: 0.8654 (p90) outliers start: 21 outliers final: 15 residues processed: 84 average time/residue: 0.1683 time to fit residues: 19.3059 Evaluate side-chains 82 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 693 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 851 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 69 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5962 Z= 0.301 Angle : 0.679 12.888 8112 Z= 0.376 Chirality : 0.045 0.184 917 Planarity : 0.006 0.115 1019 Dihedral : 9.608 73.745 904 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.02 % Allowed : 15.60 % Favored : 81.38 % 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 (0.31), residues: 721 helix: 0.52 (0.39), residues: 200 sheet: -1.93 (0.40), residues: 146 loop : -2.30 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 623 HIS 0.006 0.001 HIS A 368 PHE 0.019 0.002 PHE A 852 TYR 0.016 0.002 TYR A 859 ARG 0.006 0.000 ARG A 665 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 0.729 Fit side-chains REVERT: A 465 PHE cc_start: 0.8597 (m-80) cc_final: 0.8183 (m-80) REVERT: A 605 TRP cc_start: 0.8870 (p90) cc_final: 0.8636 (p90) REVERT: A 687 VAL cc_start: 0.9213 (t) cc_final: 0.8936 (m) outliers start: 18 outliers final: 14 residues processed: 83 average time/residue: 0.1606 time to fit residues: 18.4452 Evaluate side-chains 83 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 693 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 761 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 0.0770 chunk 54 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5962 Z= 0.158 Angle : 0.645 12.797 8112 Z= 0.359 Chirality : 0.044 0.154 917 Planarity : 0.005 0.114 1019 Dihedral : 9.540 73.492 904 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.85 % Allowed : 16.44 % Favored : 81.71 % 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: -1.85 (0.32), residues: 721 helix: 0.84 (0.40), residues: 194 sheet: -1.81 (0.41), residues: 146 loop : -2.15 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 623 HIS 0.006 0.001 HIS A 368 PHE 0.015 0.001 PHE A 406 TYR 0.017 0.001 TYR A 859 ARG 0.007 0.000 ARG A 665 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8581 (m-80) cc_final: 0.8151 (m-80) REVERT: A 687 VAL cc_start: 0.9163 (t) cc_final: 0.8931 (m) outliers start: 11 outliers final: 7 residues processed: 81 average time/residue: 0.1780 time to fit residues: 19.5877 Evaluate side-chains 78 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 851 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5962 Z= 0.213 Angle : 0.659 12.657 8112 Z= 0.365 Chirality : 0.044 0.157 917 Planarity : 0.005 0.115 1019 Dihedral : 9.579 73.627 904 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.85 % Allowed : 17.11 % Favored : 81.04 % 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: -1.82 (0.32), residues: 721 helix: 0.84 (0.40), residues: 195 sheet: -1.75 (0.41), residues: 146 loop : -2.15 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 605 HIS 0.005 0.001 HIS A 368 PHE 0.016 0.002 PHE A 852 TYR 0.017 0.001 TYR A 244 ARG 0.006 0.000 ARG A 665 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8625 (m-80) cc_final: 0.8189 (m-80) REVERT: A 687 VAL cc_start: 0.9164 (t) cc_final: 0.8937 (m) outliers start: 11 outliers final: 9 residues processed: 77 average time/residue: 0.1870 time to fit residues: 19.3806 Evaluate side-chains 80 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 851 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 5 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 943 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5962 Z= 0.263 Angle : 0.690 16.928 8112 Z= 0.377 Chirality : 0.044 0.159 917 Planarity : 0.005 0.115 1019 Dihedral : 9.771 73.702 904 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.85 % Allowed : 17.28 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.84 (0.32), residues: 721 helix: 0.87 (0.40), residues: 195 sheet: -1.81 (0.41), residues: 146 loop : -2.17 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 605 HIS 0.004 0.001 HIS A 368 PHE 0.012 0.002 PHE A 406 TYR 0.016 0.001 TYR A 244 ARG 0.006 0.000 ARG A 665 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8608 (m-80) cc_final: 0.8169 (m-80) REVERT: A 687 VAL cc_start: 0.9197 (t) cc_final: 0.8964 (m) outliers start: 11 outliers final: 11 residues processed: 79 average time/residue: 0.2151 time to fit residues: 23.2995 Evaluate side-chains 81 residues out of total 655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 693 ASP Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 851 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 7.9990 chunk 8 optimal weight: 40.0000 chunk 15 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 0.0270 chunk 41 optimal weight: 20.0000 overall best weight: 3.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.121690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.092432 restraints weight = 10591.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.094925 restraints weight = 7298.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.096475 restraints weight = 5035.378| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5962 Z= 0.211 Angle : 0.684 19.561 8112 Z= 0.370 Chirality : 0.044 0.155 917 Planarity : 0.005 0.115 1019 Dihedral : 9.767 73.625 904 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.85 % Allowed : 17.28 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.75 (0.32), residues: 721 helix: 0.85 (0.40), residues: 197 sheet: -1.57 (0.40), residues: 151 loop : -2.16 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 605 HIS 0.004 0.001 HIS A 368 PHE 0.020 0.002 PHE A 627 TYR 0.016 0.001 TYR A 408 ARG 0.006 0.000 ARG A 665 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1300.85 seconds wall clock time: 24 minutes 32.06 seconds (1472.06 seconds total)