Starting phenix.real_space_refine on Tue Dec 12 18:41:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcc_29930/12_2023/8gcc_29930_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcc_29930/12_2023/8gcc_29930.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcc_29930/12_2023/8gcc_29930_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcc_29930/12_2023/8gcc_29930_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcc_29930/12_2023/8gcc_29930_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcc_29930/12_2023/8gcc_29930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcc_29930/12_2023/8gcc_29930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcc_29930/12_2023/8gcc_29930_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcc_29930/12_2023/8gcc_29930_updated.pdb" } resolution = 2.94 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= -0.000 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 48 5.49 5 S 36 5.16 5 C 7393 2.51 5 N 2064 2.21 5 O 2158 1.98 5 F 6 1.80 5 H 10631 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 638": "OE1" <-> "OE2" Residue "A GLU 723": "OE1" <-> "OE2" Residue "A TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 638": "OE1" <-> "OE2" Residue "B GLU 723": "OE1" <-> "OE2" Residue "B TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 830": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 22336 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 10371 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 25, 'TRANS': 681} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 18, 'GLU:plan': 30, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 304 Chain: "B" Number of atoms: 10379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 10379 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 25, 'TRANS': 681} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 330 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 18, 'GLU:plan': 30, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 301 Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 764 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "D" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 764 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'YWX': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'YWX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.92, per 1000 atoms: 0.49 Number of scatterers: 22336 At special positions: 0 Unit cell: (93.795, 109.005, 114.075, 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 36 16.00 P 48 15.00 F 6 9.00 O 2158 8.00 N 2064 7.00 C 7393 6.00 H 10631 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.95 Conformation dependent library (CDL) restraints added in 2.3 seconds 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 10 sheets defined 46.5% alpha, 6.4% beta 24 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 13.63 Creating SS restraints... Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 437 through 448 removed outlier: 3.639A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA A 447 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 478 through 487 Processing helix chain 'A' and resid 514 through 530 Processing helix chain 'A' and resid 569 through 585 removed outlier: 6.204A pdb=" N ASP A 581 " --> pdb=" O ASN A 577 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ARG A 584 " --> pdb=" O GLY A 580 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASN A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 622 through 630 Processing helix chain 'A' and resid 636 through 647 Processing helix chain 'A' and resid 665 through 684 removed outlier: 4.913A pdb=" N ILE A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEU A 675 " --> pdb=" O LYS A 671 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 705 Processing helix chain 'A' and resid 714 through 724 Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 784 through 787 No H-bonds generated for 'chain 'A' and resid 784 through 787' Processing helix chain 'A' and resid 791 through 794 Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 839 through 851 Processing helix chain 'A' and resid 902 through 914 Processing helix chain 'A' and resid 938 through 947 Processing helix chain 'A' and resid 950 through 953 No H-bonds generated for 'chain 'A' and resid 950 through 953' Processing helix chain 'A' and resid 980 through 1024 Processing helix chain 'A' and resid 1035 through 1044 Processing helix chain 'A' and resid 1104 through 1110 Processing helix chain 'A' and resid 1119 through 1121 No H-bonds generated for 'chain 'A' and resid 1119 through 1121' Processing helix chain 'A' and resid 1124 through 1146 removed outlier: 3.564A pdb=" N LYS A1146 " --> pdb=" O ALA A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1176 Proline residue: A1162 - end of helix Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 437 through 448 removed outlier: 3.633A pdb=" N ALA B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA B 447 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 453 No H-bonds generated for 'chain 'B' and resid 451 through 453' Processing helix chain 'B' and resid 471 through 475 Processing helix chain 'B' and resid 478 through 487 Processing helix chain 'B' and resid 514 through 530 Processing helix chain 'B' and resid 532 through 535 No H-bonds generated for 'chain 'B' and resid 532 through 535' Processing helix chain 'B' and resid 569 through 585 removed outlier: 6.217A pdb=" N ASP B 581 " --> pdb=" O ASN B 577 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG B 584 " --> pdb=" O GLY B 580 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASN B 585 " --> pdb=" O ASP B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 607 Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 622 through 630 Processing helix chain 'B' and resid 636 through 647 Processing helix chain 'B' and resid 665 through 684 removed outlier: 4.918A pdb=" N ILE B 674 " --> pdb=" O ASP B 670 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU B 675 " --> pdb=" O LYS B 671 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 676 " --> pdb=" O GLU B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 705 Processing helix chain 'B' and resid 714 through 724 Processing helix chain 'B' and resid 731 through 742 Processing helix chain 'B' and resid 784 through 787 No H-bonds generated for 'chain 'B' and resid 784 through 787' Processing helix chain 'B' and resid 791 through 794 Processing helix chain 'B' and resid 817 through 821 Processing helix chain 'B' and resid 839 through 851 Processing helix chain 'B' and resid 902 through 914 Processing helix chain 'B' and resid 938 through 947 Processing helix chain 'B' and resid 950 through 953 No H-bonds generated for 'chain 'B' and resid 950 through 953' Processing helix chain 'B' and resid 980 through 1025 Processing helix chain 'B' and resid 1035 through 1044 Processing helix chain 'B' and resid 1104 through 1110 Processing helix chain 'B' and resid 1112 through 1115 No H-bonds generated for 'chain 'B' and resid 1112 through 1115' Processing helix chain 'B' and resid 1119 through 1121 No H-bonds generated for 'chain 'B' and resid 1119 through 1121' Processing helix chain 'B' and resid 1124 through 1146 removed outlier: 3.567A pdb=" N LYS B1146 " --> pdb=" O ALA B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1149 through 1176 Proline residue: B1162 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 454 through 456 removed outlier: 6.510A pdb=" N THR A 429 " --> pdb=" O GLY A 455 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N HIS A 505 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 754 through 757 Processing sheet with id= C, first strand: chain 'A' and resid 957 through 961 removed outlier: 6.502A pdb=" N VAL A 878 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU A 871 " --> pdb=" O VAL A 878 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR A 880 " --> pdb=" O ILE A 869 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE A 869 " --> pdb=" O THR A 880 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 883 through 885 Processing sheet with id= E, first strand: chain 'A' and resid 965 through 968 removed outlier: 4.328A pdb=" N ILE A 965 " --> pdb=" O TYR A 977 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 454 through 456 removed outlier: 6.589A pdb=" N THR B 429 " --> pdb=" O GLY B 455 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N HIS B 505 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 754 through 757 Processing sheet with id= H, first strand: chain 'B' and resid 957 through 961 removed outlier: 6.355A pdb=" N VAL B 878 " --> pdb=" O GLU B 871 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU B 871 " --> pdb=" O VAL B 878 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR B 880 " --> pdb=" O ILE B 869 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ILE B 869 " --> pdb=" O THR B 880 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 883 through 885 Processing sheet with id= J, first strand: chain 'B' and resid 965 through 968 removed outlier: 4.327A pdb=" N ILE B 965 " --> pdb=" O TYR B 977 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 8.98 Time building geometry restraints manager: 19.42 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: 10623 1.03 - 1.23: 50 1.23 - 1.42: 5178 1.42 - 1.62: 6781 1.62 - 1.81: 62 Bond restraints: 22694 Sorted by residual: bond pdb=" C17 YWX C 101 " pdb=" C6 YWX C 101 " ideal model delta sigma weight residual 1.154 1.395 -0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C17 YWX D 101 " pdb=" C6 YWX D 101 " ideal model delta sigma weight residual 1.154 1.394 -0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C5 YWX D 101 " pdb=" C6 YWX D 101 " ideal model delta sigma weight residual 1.285 1.521 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C5 YWX C 101 " pdb=" C6 YWX C 101 " ideal model delta sigma weight residual 1.285 1.519 -0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C17 YWX D 101 " pdb=" C18 YWX D 101 " ideal model delta sigma weight residual 1.285 1.501 -0.216 2.00e-02 2.50e+03 1.16e+02 ... (remaining 22689 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.34: 527 106.34 - 113.25: 25286 113.25 - 120.16: 7677 120.16 - 127.07: 7103 127.07 - 133.98: 229 Bond angle restraints: 40822 Sorted by residual: angle pdb=" C10 YWX D 101 " pdb=" C15 YWX D 101 " pdb=" F1 YWX D 101 " ideal model delta sigma weight residual 80.33 112.65 -32.32 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C10 YWX C 101 " pdb=" C15 YWX C 101 " pdb=" F1 YWX C 101 " ideal model delta sigma weight residual 80.33 112.62 -32.29 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C10 YWX D 101 " pdb=" C15 YWX D 101 " pdb=" F2 YWX D 101 " ideal model delta sigma weight residual 80.33 112.46 -32.13 3.00e+00 1.11e-01 1.15e+02 angle pdb=" C10 YWX C 101 " pdb=" C15 YWX C 101 " pdb=" F2 YWX C 101 " ideal model delta sigma weight residual 80.33 112.42 -32.09 3.00e+00 1.11e-01 1.14e+02 angle pdb=" F YWX D 101 " pdb=" C15 YWX D 101 " pdb=" F2 YWX D 101 " ideal model delta sigma weight residual 80.32 106.35 -26.03 3.00e+00 1.11e-01 7.53e+01 ... (remaining 40817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.81: 9788 34.81 - 69.62: 457 69.62 - 104.43: 21 104.43 - 139.24: 0 139.24 - 174.05: 2 Dihedral angle restraints: 10268 sinusoidal: 5386 harmonic: 4882 Sorted by residual: dihedral pdb=" C4' DA C 3 " pdb=" C3' DA C 3 " pdb=" O3' DA C 3 " pdb=" P DT C 4 " ideal model delta sinusoidal sigma weight residual 220.00 45.95 174.05 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG C 2 " pdb=" C3' DG C 2 " pdb=" O3' DG C 2 " pdb=" P DA C 3 " ideal model delta sinusoidal sigma weight residual 220.00 73.89 146.11 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" CA ASP A 615 " pdb=" CB ASP A 615 " pdb=" CG ASP A 615 " pdb=" OD1 ASP A 615 " ideal model delta sinusoidal sigma weight residual -30.00 -87.99 57.99 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 10265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1152 0.027 - 0.055: 434 0.055 - 0.082: 169 0.082 - 0.109: 78 0.109 - 0.137: 31 Chirality restraints: 1864 Sorted by residual: chirality pdb=" CA ILE A 960 " pdb=" N ILE A 960 " pdb=" C ILE A 960 " pdb=" CB ILE A 960 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ILE B 893 " pdb=" N ILE B 893 " pdb=" C ILE B 893 " pdb=" CB ILE B 893 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE A 966 " pdb=" N ILE A 966 " pdb=" C ILE A 966 " pdb=" CB ILE A 966 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 1861 not shown) Planarity restraints: 3339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C YWX D 101 " -0.049 2.00e-02 2.50e+03 8.07e-02 2.12e+02 pdb=" O YWX D 101 " -0.099 2.00e-02 2.50e+03 pdb=" C1 YWX D 101 " -0.099 2.00e-02 2.50e+03 pdb=" C16 YWX D 101 " 0.069 2.00e-02 2.50e+03 pdb=" C17 YWX D 101 " 0.092 2.00e-02 2.50e+03 pdb=" C18 YWX D 101 " 0.118 2.00e-02 2.50e+03 pdb=" C5 YWX D 101 " 0.096 2.00e-02 2.50e+03 pdb=" C6 YWX D 101 " 0.050 2.00e-02 2.50e+03 pdb=" C7 YWX D 101 " -0.054 2.00e-02 2.50e+03 pdb=" C8 YWX D 101 " -0.018 2.00e-02 2.50e+03 pdb=" C9 YWX D 101 " -0.134 2.00e-02 2.50e+03 pdb=" N4 YWX D 101 " 0.048 2.00e-02 2.50e+03 pdb=" N5 YWX D 101 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C YWX C 101 " 0.010 2.00e-02 2.50e+03 2.31e-02 1.74e+01 pdb=" O YWX C 101 " 0.015 2.00e-02 2.50e+03 pdb=" C1 YWX C 101 " 0.030 2.00e-02 2.50e+03 pdb=" C16 YWX C 101 " -0.036 2.00e-02 2.50e+03 pdb=" C17 YWX C 101 " -0.032 2.00e-02 2.50e+03 pdb=" C18 YWX C 101 " -0.018 2.00e-02 2.50e+03 pdb=" C5 YWX C 101 " -0.016 2.00e-02 2.50e+03 pdb=" C6 YWX C 101 " -0.012 2.00e-02 2.50e+03 pdb=" C7 YWX C 101 " 0.013 2.00e-02 2.50e+03 pdb=" C8 YWX C 101 " -0.006 2.00e-02 2.50e+03 pdb=" C9 YWX C 101 " 0.049 2.00e-02 2.50e+03 pdb=" N4 YWX C 101 " -0.007 2.00e-02 2.50e+03 pdb=" N5 YWX C 101 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N YWX C 101 " 0.033 2.00e-02 2.50e+03 2.98e-02 1.55e+01 pdb=" C1 YWX C 101 " -0.048 2.00e-02 2.50e+03 pdb=" C2 YWX C 101 " 0.002 2.00e-02 2.50e+03 pdb=" C3 YWX C 101 " 0.013 2.00e-02 2.50e+03 pdb=" C4 YWX C 101 " -0.027 2.00e-02 2.50e+03 pdb=" N1 YWX C 101 " 0.042 2.00e-02 2.50e+03 pdb=" N2 YWX C 101 " -0.014 2.00e-02 2.50e+03 ... (remaining 3336 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1043 2.17 - 2.78: 41804 2.78 - 3.38: 62690 3.38 - 3.99: 84583 3.99 - 4.60: 130939 Nonbonded interactions: 321059 Sorted by model distance: nonbonded pdb=" O ARG A 451 " pdb="HH11 ARG A 451 " model vdw 1.560 1.850 nonbonded pdb=" O ARG B 451 " pdb="HH11 ARG B 451 " model vdw 1.560 1.850 nonbonded pdb=" HH TYR A 995 " pdb=" OD2 ASP A1156 " model vdw 1.586 1.850 nonbonded pdb=" HH TYR B 995 " pdb=" OD2 ASP B1156 " model vdw 1.587 1.850 nonbonded pdb=" O ALA B 632 " pdb="HH22 ARG B 639 " model vdw 1.599 1.850 ... (remaining 321054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 409 through 1117 or (resid 1118 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name NE or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3)) or r \ esid 1119 through 1177)) } ncs_group { reference = chain 'C' selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.360 Extract box with map and model: 12.860 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 83.950 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.110 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:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 0.241 12063 Z= 0.396 Angle : 1.038 32.318 16582 Z= 0.417 Chirality : 0.039 0.137 1864 Planarity : 0.004 0.081 1949 Dihedral : 20.020 174.051 4344 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.54 % Allowed : 18.17 % Favored : 79.29 % 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: 1.52 (0.24), residues: 1402 helix: 2.65 (0.21), residues: 672 sheet: -1.56 (0.44), residues: 158 loop : -0.19 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 642 HIS 0.003 0.001 HIS B 612 PHE 0.011 0.001 PHE B 676 TYR 0.011 0.001 TYR B1111 ARG 0.002 0.000 ARG B 451 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 25 residues processed: 131 average time/residue: 2.1761 time to fit residues: 314.0611 Evaluate side-chains 125 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 1.717 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 25 residues processed: 0 time to fit residues: 2.3437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12063 Z= 0.274 Angle : 0.741 23.795 16582 Z= 0.333 Chirality : 0.039 0.137 1864 Planarity : 0.003 0.038 1949 Dihedral : 17.675 174.129 2097 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.37 % Allowed : 16.45 % Favored : 79.19 % 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: 1.43 (0.24), residues: 1402 helix: 2.45 (0.20), residues: 688 sheet: -1.43 (0.44), residues: 154 loop : -0.22 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 642 HIS 0.003 0.001 HIS B 612 PHE 0.011 0.001 PHE B 676 TYR 0.009 0.001 TYR A 994 ARG 0.004 0.000 ARG A1033 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 110 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 24 residues processed: 152 average time/residue: 1.8736 time to fit residues: 320.9738 Evaluate side-chains 131 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 1.787 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 2.2946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.0281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12063 Z= 0.258 Angle : 0.736 23.674 16582 Z= 0.331 Chirality : 0.039 0.138 1864 Planarity : 0.003 0.033 1949 Dihedral : 17.649 174.035 2097 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.26 % Allowed : 16.04 % Favored : 79.70 % 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: 1.49 (0.24), residues: 1402 helix: 2.55 (0.20), residues: 684 sheet: -1.41 (0.45), residues: 154 loop : -0.24 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 642 HIS 0.003 0.001 HIS B 612 PHE 0.011 0.001 PHE A 676 TYR 0.009 0.001 TYR B 994 ARG 0.003 0.000 ARG A1033 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 112 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 27 residues processed: 154 average time/residue: 1.8895 time to fit residues: 325.6752 Evaluate side-chains 136 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 1.545 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 27 residues processed: 0 time to fit residues: 2.1409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B 920 GLN B1166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.0348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12063 Z= 0.267 Angle : 0.739 23.825 16582 Z= 0.332 Chirality : 0.039 0.137 1864 Planarity : 0.003 0.030 1949 Dihedral : 17.660 173.875 2097 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.86 % Allowed : 16.55 % Favored : 79.59 % 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: 1.45 (0.24), residues: 1402 helix: 2.52 (0.20), residues: 684 sheet: -1.44 (0.44), residues: 154 loop : -0.27 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 642 HIS 0.003 0.001 HIS B 612 PHE 0.011 0.001 PHE B 676 TYR 0.009 0.001 TYR B 994 ARG 0.002 0.000 ARG A1033 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 116 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 25 residues processed: 152 average time/residue: 1.8218 time to fit residues: 309.5193 Evaluate side-chains 132 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 1.641 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 25 residues processed: 0 time to fit residues: 2.0977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.0540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12063 Z= 0.373 Angle : 0.766 23.649 16582 Z= 0.351 Chirality : 0.041 0.141 1864 Planarity : 0.004 0.035 1949 Dihedral : 17.778 172.925 2097 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.16 % Allowed : 16.75 % Favored : 79.09 % 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: 1.15 (0.23), residues: 1402 helix: 2.29 (0.20), residues: 684 sheet: -1.64 (0.44), residues: 154 loop : -0.40 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 642 HIS 0.004 0.001 HIS B 612 PHE 0.013 0.001 PHE A 676 TYR 0.011 0.002 TYR A 994 ARG 0.002 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 113 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 24 residues processed: 154 average time/residue: 1.8797 time to fit residues: 324.9310 Evaluate side-chains 136 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.742 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 2.1743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 134 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.0512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12063 Z= 0.240 Angle : 0.737 23.884 16582 Z= 0.332 Chirality : 0.039 0.138 1864 Planarity : 0.003 0.030 1949 Dihedral : 17.695 173.686 2097 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.45 % Allowed : 17.77 % Favored : 78.78 % 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: 1.40 (0.24), residues: 1402 helix: 2.49 (0.20), residues: 684 sheet: -1.51 (0.46), residues: 144 loop : -0.32 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 642 HIS 0.003 0.001 HIS B 612 PHE 0.011 0.001 PHE B 676 TYR 0.008 0.001 TYR B 994 ARG 0.002 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 119 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 24 residues processed: 153 average time/residue: 1.9645 time to fit residues: 335.1294 Evaluate side-chains 138 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 1.752 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 2.1023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.0370 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12063 Z= 0.221 Angle : 0.730 23.838 16582 Z= 0.327 Chirality : 0.039 0.137 1864 Planarity : 0.003 0.028 1949 Dihedral : 17.659 173.738 2097 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.35 % Allowed : 17.77 % Favored : 78.88 % 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: 1.49 (0.24), residues: 1402 helix: 2.62 (0.21), residues: 684 sheet: -1.84 (0.47), residues: 124 loop : -0.30 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 642 HIS 0.002 0.001 HIS B 612 PHE 0.011 0.001 PHE B 676 TYR 0.007 0.001 TYR B 994 ARG 0.002 0.000 ARG A 970 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 26 residues processed: 149 average time/residue: 2.0489 time to fit residues: 340.1743 Evaluate side-chains 134 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 1.691 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 26 residues processed: 0 time to fit residues: 2.0996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12063 Z= 0.201 Angle : 0.727 23.856 16582 Z= 0.325 Chirality : 0.038 0.137 1864 Planarity : 0.003 0.026 1949 Dihedral : 17.625 173.780 2097 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.15 % Allowed : 18.17 % Favored : 78.68 % 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: 1.59 (0.24), residues: 1402 helix: 2.71 (0.21), residues: 684 sheet: -1.78 (0.48), residues: 124 loop : -0.27 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 642 HIS 0.002 0.000 HIS B 612 PHE 0.010 0.001 PHE B 676 TYR 0.007 0.001 TYR B 591 ARG 0.002 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 114 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 26 residues processed: 144 average time/residue: 2.0098 time to fit residues: 321.4216 Evaluate side-chains 134 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 1.661 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 26 residues processed: 0 time to fit residues: 2.1217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 116 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12063 Z= 0.254 Angle : 0.739 23.753 16582 Z= 0.333 Chirality : 0.039 0.137 1864 Planarity : 0.003 0.027 1949 Dihedral : 17.665 173.196 2097 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.05 % Allowed : 18.58 % Favored : 78.38 % 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: 1.50 (0.24), residues: 1402 helix: 2.61 (0.20), residues: 684 sheet: -1.49 (0.46), residues: 144 loop : -0.30 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 642 HIS 0.003 0.001 HIS B 612 PHE 0.011 0.001 PHE B 676 TYR 0.009 0.001 TYR B 994 ARG 0.002 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 25 residues processed: 145 average time/residue: 1.9521 time to fit residues: 317.7882 Evaluate side-chains 134 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 1.723 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 25 residues processed: 0 time to fit residues: 2.1875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 114 optimal weight: 0.0040 chunk 11 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.0556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12063 Z= 0.291 Angle : 0.750 23.734 16582 Z= 0.340 Chirality : 0.040 0.137 1864 Planarity : 0.003 0.029 1949 Dihedral : 17.705 172.983 2097 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.54 % Allowed : 19.39 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.40 (0.24), residues: 1402 helix: 2.52 (0.20), residues: 684 sheet: -1.55 (0.46), residues: 144 loop : -0.34 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 642 HIS 0.003 0.001 HIS B 612 PHE 0.011 0.001 PHE A 676 TYR 0.009 0.001 TYR B 994 ARG 0.002 0.000 ARG B 774 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue TYR 424 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue LYS 439 is missing expected H atoms. Skipping. Residue THR 443 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue VAL 448 is missing expected H atoms. Skipping. Residue LYS 449 is missing expected H atoms. Skipping. Residue LEU 471 is missing expected H atoms. Skipping. Residue MET 475 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue LYS 494 is missing expected H atoms. Skipping. Residue VAL 549 is missing expected H atoms. Skipping. Residue LYS 576 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LYS 592 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Residue LYS 633 is missing expected H atoms. Skipping. Residue THR 650 is missing expected H atoms. Skipping. Residue VAL 652 is missing expected H atoms. Skipping. Residue SER 655 is missing expected H atoms. Skipping. Residue VAL 890 is missing expected H atoms. Skipping. Residue LYS 907 is missing expected H atoms. Skipping. Residue LYS 915 is missing expected H atoms. Skipping. Residue VAL 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue LEU 936 is missing expected H atoms. Skipping. Residue VAL 940 is missing expected H atoms. Skipping. Residue LEU 941 is missing expected H atoms. Skipping. Residue VAL 945 is missing expected H atoms. Skipping. Residue LYS 1036 is missing expected H atoms. Skipping. Residue MET 1104 is missing expected H atoms. Skipping. Residue SER 1132 is missing expected H atoms. Skipping. Residue LYS 1136 is missing expected H atoms. Skipping. Residue LYS 1146 is missing expected H atoms. Skipping. Residue LYS 1173 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 25 residues processed: 136 average time/residue: 1.7962 time to fit residues: 274.9024 Evaluate side-chains 133 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 1.682 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 25 residues processed: 0 time to fit residues: 2.1683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B1166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120972 restraints weight = 37107.069| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.41 r_work: 0.3268 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.0558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12063 Z= 0.243 Angle : 0.740 23.803 16582 Z= 0.334 Chirality : 0.039 0.137 1864 Planarity : 0.003 0.028 1949 Dihedral : 17.675 173.306 2097 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.84 % Allowed : 18.98 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.48 (0.24), residues: 1402 helix: 2.60 (0.20), residues: 684 sheet: -1.51 (0.46), residues: 144 loop : -0.32 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 642 HIS 0.003 0.001 HIS B 612 PHE 0.011 0.001 PHE A 676 TYR 0.008 0.001 TYR B 994 ARG 0.002 0.000 ARG B 774 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7271.61 seconds wall clock time: 128 minutes 3.05 seconds (7683.05 seconds total)