Starting phenix.real_space_refine on Thu Sep 26 14:20:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzo_0559/09_2024/6nzo_0559.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzo_0559/09_2024/6nzo_0559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzo_0559/09_2024/6nzo_0559.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzo_0559/09_2024/6nzo_0559.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzo_0559/09_2024/6nzo_0559.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzo_0559/09_2024/6nzo_0559.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 290 5.49 5 S 32 5.16 5 C 7707 2.51 5 N 2563 2.21 5 O 3143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13738 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 797 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 834 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 792 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 752 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "S" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1816 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "S" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12284 SG CYS S 143 60.709 80.388 47.265 1.00109.22 S ATOM 12396 SG CYS S 158 59.164 84.192 47.848 1.00101.19 S ATOM 12429 SG CYS S 163 61.766 82.563 50.683 1.00113.64 S ATOM 12466 SG CYS S 169 61.843 82.802 46.265 1.00112.25 S ATOM 12173 SG CYS S 129 58.781 80.486 51.064 1.00112.66 S ATOM 12187 SG CYS S 131 58.804 77.494 49.481 1.00118.61 S ATOM 12284 SG CYS S 143 60.709 80.388 47.265 1.00109.22 S ATOM 12325 SG CYS S 149 58.199 78.606 47.178 1.00 92.28 S ATOM 13234 SG CYS S 261 37.901 89.429 19.020 1.00124.70 S ATOM 13613 SG CYS S 308 40.146 91.851 16.557 1.00133.16 S ATOM 13631 SG CYS S 310 40.500 89.796 15.425 1.00135.88 S ATOM 13665 SG CYS S 315 37.577 90.841 15.137 1.00131.95 S Time building chain proxies: 8.44, per 1000 atoms: 0.61 Number of scatterers: 13738 At special positions: 0 Unit cell: (83.2, 146.64, 131.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 32 16.00 P 290 15.00 O 3143 8.00 N 2563 7.00 C 7707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S1001 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 169 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 143 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 158 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 163 " pdb=" ZN S1002 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 129 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 149 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 143 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 131 " pdb=" ZN S1003 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 308 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 315 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 310 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 261 " Number of angles added : 18 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 14 sheets defined 58.8% alpha, 5.8% beta 143 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 6.85 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.962A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.552A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.718A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 17 through 21' Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.561A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.633A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.003A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.501A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.926A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.392A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.521A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.546A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 151 through 155 removed outlier: 3.601A pdb=" N LYS S 155 " --> pdb=" O ARG S 152 " (cutoff:3.500A) Processing helix chain 'S' and resid 215 through 230 Processing helix chain 'S' and resid 252 through 256 removed outlier: 3.607A pdb=" N ARG S 255 " --> pdb=" O ASN S 252 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE S 256 " --> pdb=" O LEU S 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 252 through 256' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.828A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.107A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.726A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AA8, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.271A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.082A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'S' and resid 182 through 187 Processing sheet with id=AB4, first strand: chain 'S' and resid 205 through 208 removed outlier: 6.715A pdb=" N PHE S 205 " --> pdb=" O ALA S 282 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA S 282 " --> pdb=" O PHE S 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 212 through 214 443 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 5.46 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2233 1.33 - 1.45: 4991 1.45 - 1.57: 6723 1.57 - 1.69: 578 1.69 - 1.81: 46 Bond restraints: 14571 Sorted by residual: bond pdb=" C ASP S 134 " pdb=" N TRP S 135 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.23e-02 6.61e+03 2.32e+01 bond pdb=" C ILE G 79 " pdb=" N PRO G 80 " ideal model delta sigma weight residual 1.334 1.392 -0.058 1.51e-02 4.39e+03 1.45e+01 bond pdb=" C3' DC I 143 " pdb=" O3' DC I 143 " ideal model delta sigma weight residual 1.422 1.500 -0.078 3.00e-02 1.11e+03 6.72e+00 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.495 -0.073 3.00e-02 1.11e+03 5.95e+00 bond pdb=" C ILE E 51 " pdb=" N ARG E 52 " ideal model delta sigma weight residual 1.335 1.366 -0.032 1.36e-02 5.41e+03 5.42e+00 ... (remaining 14566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 19986 2.05 - 4.10: 856 4.10 - 6.15: 49 6.15 - 8.20: 15 8.20 - 10.25: 3 Bond angle restraints: 20909 Sorted by residual: angle pdb=" N PRO S 88 " pdb=" CA PRO S 88 " pdb=" CB PRO S 88 " ideal model delta sigma weight residual 103.00 110.43 -7.43 1.10e+00 8.26e-01 4.56e+01 angle pdb=" N PRO S 89 " pdb=" CA PRO S 89 " pdb=" CB PRO S 89 " ideal model delta sigma weight residual 103.38 110.40 -7.02 1.05e+00 9.07e-01 4.47e+01 angle pdb=" N PRO S 84 " pdb=" CA PRO S 84 " pdb=" CB PRO S 84 " ideal model delta sigma weight residual 103.00 110.24 -7.24 1.10e+00 8.26e-01 4.33e+01 angle pdb=" C SER S 122 " pdb=" N ASP S 123 " pdb=" CA ASP S 123 " ideal model delta sigma weight residual 122.61 129.82 -7.21 1.56e+00 4.11e-01 2.14e+01 angle pdb=" N VAL S 159 " pdb=" CA VAL S 159 " pdb=" C VAL S 159 " ideal model delta sigma weight residual 110.05 105.60 4.45 1.09e+00 8.42e-01 1.67e+01 ... (remaining 20904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.58: 6484 34.58 - 69.17: 1505 69.17 - 103.75: 15 103.75 - 138.33: 0 138.33 - 172.91: 4 Dihedral angle restraints: 8008 sinusoidal: 5161 harmonic: 2847 Sorted by residual: dihedral pdb=" CA GLN S 172 " pdb=" C GLN S 172 " pdb=" N ARG S 173 " pdb=" CA ARG S 173 " ideal model delta harmonic sigma weight residual 180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA GLU S 133 " pdb=" C GLU S 133 " pdb=" N ASP S 134 " pdb=" CA ASP S 134 " ideal model delta harmonic sigma weight residual 180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 47.09 172.91 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1700 0.056 - 0.112: 531 0.112 - 0.168: 91 0.168 - 0.224: 23 0.224 - 0.280: 6 Chirality restraints: 2351 Sorted by residual: chirality pdb=" CB ILE H 51 " pdb=" CA ILE H 51 " pdb=" CG1 ILE H 51 " pdb=" CG2 ILE H 51 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE G 111 " pdb=" CA ILE G 111 " pdb=" CG1 ILE G 111 " pdb=" CG2 ILE G 111 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA GLU S 216 " pdb=" N GLU S 216 " pdb=" C GLU S 216 " pdb=" CB GLU S 216 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 2348 not shown) Planarity restraints: 1659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 102 " -0.038 2.00e-02 2.50e+03 1.77e-02 9.39e+00 pdb=" N9 DG I 102 " 0.032 2.00e-02 2.50e+03 pdb=" C8 DG I 102 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 102 " 0.023 2.00e-02 2.50e+03 pdb=" C5 DG I 102 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 102 " -0.021 2.00e-02 2.50e+03 pdb=" O6 DG I 102 " -0.012 2.00e-02 2.50e+03 pdb=" N1 DG I 102 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DG I 102 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 102 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DG I 102 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG I 102 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " -0.040 2.00e-02 2.50e+03 1.78e-02 8.71e+00 pdb=" N9 DA I 20 " 0.039 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.007 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " -0.012 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 106 " 0.037 2.00e-02 2.50e+03 1.61e-02 7.82e+00 pdb=" N9 DG J 106 " -0.038 2.00e-02 2.50e+03 pdb=" C8 DG J 106 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG J 106 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG J 106 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DG J 106 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG J 106 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DG J 106 " 0.007 2.00e-02 2.50e+03 pdb=" C2 DG J 106 " -0.010 2.00e-02 2.50e+03 pdb=" N2 DG J 106 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG J 106 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG J 106 " -0.004 2.00e-02 2.50e+03 ... (remaining 1656 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3615 2.83 - 3.35: 11979 3.35 - 3.87: 27098 3.87 - 4.38: 30302 4.38 - 4.90: 43766 Nonbonded interactions: 116760 Sorted by model distance: nonbonded pdb=" O CYS S 129 " pdb=" ND2 ASN S 164 " model vdw 2.313 3.120 nonbonded pdb=" O SER D 120 " pdb=" OG SER D 120 " model vdw 2.322 3.040 nonbonded pdb=" O SER S 260 " pdb=" ND2 ASN S 295 " model vdw 2.333 3.120 nonbonded pdb=" CB THR H 29 " pdb=" OP1 DT I 104 " model vdw 2.333 3.470 nonbonded pdb=" O LYS S 190 " pdb=" ND2 ASN S 258 " model vdw 2.352 3.120 ... (remaining 116755 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = (chain 'B' and resid 24 through 100) selection = (chain 'F' and resid 24 through 100) } ncs_group { reference = (chain 'C' and resid 16 through 118) selection = (chain 'G' and (resid 16 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = (chain 'D' and resid 26 through 120) selection = chain 'H' } 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=0.89 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 40.840 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 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 0.078 14571 Z= 0.401 Angle : 0.926 10.246 20909 Z= 0.563 Chirality : 0.056 0.280 2351 Planarity : 0.007 0.056 1659 Dihedral : 27.022 172.914 6176 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.79 % Favored : 95.11 % Rotamer: Outliers : 0.12 % Allowed : 5.88 % Favored : 94.00 % 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: -1.08 (0.24), residues: 961 helix: 0.15 (0.19), residues: 551 sheet: -2.07 (0.76), residues: 45 loop : -1.82 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP S 135 HIS 0.003 0.001 HIS G 31 PHE 0.024 0.003 PHE B 61 TYR 0.016 0.003 TYR H 118 ARG 0.007 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 54 TYR cc_start: 0.7762 (m-80) cc_final: 0.7551 (m-10) REVERT: G 102 ILE cc_start: 0.9044 (mt) cc_final: 0.8705 (mm) REVERT: H 27 ARG cc_start: 0.7646 (mmm160) cc_final: 0.6481 (ptp-170) REVERT: H 37 TYR cc_start: 0.8260 (m-80) cc_final: 0.8017 (m-80) REVERT: H 42 LEU cc_start: 0.8182 (tp) cc_final: 0.7827 (tp) REVERT: H 56 MET cc_start: 0.7288 (tpp) cc_final: 0.7018 (mmp) REVERT: H 68 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6901 (tm-30) REVERT: S 201 GLN cc_start: 0.8295 (tt0) cc_final: 0.7894 (tp40) outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.3805 time to fit residues: 128.5739 Evaluate side-chains 165 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 0.0870 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 110 optimal weight: 0.2980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS B 93 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 106 HIS E 39 HIS E 68 GLN E 85 GLN F 75 HIS G 24 GLN G 38 ASN H 106 HIS S 215 ASN S 242 ASN ** S 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 295 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14571 Z= 0.186 Angle : 0.585 7.175 20909 Z= 0.347 Chirality : 0.035 0.152 2351 Planarity : 0.005 0.062 1659 Dihedral : 29.893 172.339 4260 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.82 % Allowed : 12.61 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.27), residues: 961 helix: 1.92 (0.21), residues: 559 sheet: -1.70 (0.80), residues: 45 loop : -1.42 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 135 HIS 0.007 0.001 HIS B 75 PHE 0.009 0.001 PHE B 61 TYR 0.015 0.002 TYR G 57 ARG 0.009 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 213 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 THR cc_start: 0.8102 (p) cc_final: 0.7782 (t) REVERT: B 84 MET cc_start: 0.7698 (mmm) cc_final: 0.7300 (ptm) REVERT: G 102 ILE cc_start: 0.8983 (mt) cc_final: 0.8763 (mm) REVERT: H 27 ARG cc_start: 0.7698 (mmm160) cc_final: 0.6469 (ptp-170) REVERT: H 28 LYS cc_start: 0.7560 (tttm) cc_final: 0.7264 (mmtt) REVERT: H 37 TYR cc_start: 0.8068 (m-80) cc_final: 0.7707 (m-80) REVERT: H 68 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7054 (tm-30) REVERT: H 79 HIS cc_start: 0.7839 (t70) cc_final: 0.7500 (t70) REVERT: S 150 ILE cc_start: 0.8857 (tp) cc_final: 0.8606 (pt) REVERT: S 154 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8105 (m) REVERT: S 167 GLU cc_start: 0.7008 (pm20) cc_final: 0.6799 (pm20) REVERT: S 244 PHE cc_start: 0.5545 (m-80) cc_final: 0.5021 (m-80) outliers start: 23 outliers final: 13 residues processed: 224 average time/residue: 0.3056 time to fit residues: 93.4879 Evaluate side-chains 191 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 177 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain S residue 218 THR Chi-restraints excluded: chain S residue 223 MET Chi-restraints excluded: chain S residue 256 PHE Chi-restraints excluded: chain S residue 272 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 30 optimal weight: 0.0570 chunk 110 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 14571 Z= 0.413 Angle : 0.735 7.492 20909 Z= 0.423 Chirality : 0.043 0.185 2351 Planarity : 0.006 0.061 1659 Dihedral : 30.405 176.467 4260 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.77 % Allowed : 17.01 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 961 helix: 1.34 (0.21), residues: 553 sheet: -1.62 (0.83), residues: 45 loop : -1.47 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP S 135 HIS 0.007 0.002 HIS S 141 PHE 0.026 0.003 PHE E 67 TYR 0.017 0.003 TYR H 37 ARG 0.006 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 197 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8894 (tp-100) cc_final: 0.7943 (tm-30) REVERT: D 59 MET cc_start: 0.8323 (tpp) cc_final: 0.8070 (tpp) REVERT: D 68 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7372 (tm-30) REVERT: E 109 LEU cc_start: 0.7698 (tt) cc_final: 0.7488 (tt) REVERT: F 92 ARG cc_start: 0.6512 (tpt-90) cc_final: 0.6131 (tpp80) REVERT: F 100 PHE cc_start: 0.7935 (m-80) cc_final: 0.7187 (m-10) REVERT: G 102 ILE cc_start: 0.9086 (mt) cc_final: 0.8826 (mm) REVERT: H 27 ARG cc_start: 0.8000 (mmm160) cc_final: 0.6665 (ptp-170) REVERT: H 28 LYS cc_start: 0.7598 (tttm) cc_final: 0.7377 (mmtt) REVERT: H 68 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7440 (tm-30) REVERT: S 109 ILE cc_start: 0.4639 (pt) cc_final: 0.4209 (pt) REVERT: S 214 ILE cc_start: 0.5247 (OUTLIER) cc_final: 0.4998 (pt) outliers start: 39 outliers final: 27 residues processed: 217 average time/residue: 0.2845 time to fit residues: 86.8271 Evaluate side-chains 206 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 178 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain S residue 170 GLN Chi-restraints excluded: chain S residue 214 ILE Chi-restraints excluded: chain S residue 265 CYS Chi-restraints excluded: chain S residue 272 VAL Chi-restraints excluded: chain S residue 278 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 111 optimal weight: 0.0570 chunk 117 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 overall best weight: 2.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14571 Z= 0.286 Angle : 0.652 10.195 20909 Z= 0.378 Chirality : 0.038 0.171 2351 Planarity : 0.005 0.060 1659 Dihedral : 30.286 175.475 4260 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.02 % Allowed : 19.09 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.27), residues: 961 helix: 1.56 (0.21), residues: 554 sheet: -1.06 (0.97), residues: 28 loop : -1.54 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP S 135 HIS 0.007 0.001 HIS S 141 PHE 0.027 0.002 PHE E 67 TYR 0.023 0.002 TYR H 80 ARG 0.006 0.000 ARG S 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 191 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8849 (tp-100) cc_final: 0.7946 (tm-30) REVERT: D 68 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7392 (tm-30) REVERT: D 79 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.7535 (t70) REVERT: F 92 ARG cc_start: 0.6395 (tpt-90) cc_final: 0.6115 (tpp80) REVERT: F 100 PHE cc_start: 0.7941 (m-80) cc_final: 0.7739 (m-10) REVERT: G 104 GLN cc_start: 0.8454 (mp10) cc_final: 0.8217 (mp10) REVERT: H 27 ARG cc_start: 0.7964 (mmm160) cc_final: 0.6688 (ptp-170) REVERT: H 68 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7342 (tm-30) outliers start: 41 outliers final: 32 residues processed: 213 average time/residue: 0.2706 time to fit residues: 81.5858 Evaluate side-chains 209 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 176 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain S residue 170 GLN Chi-restraints excluded: chain S residue 218 THR Chi-restraints excluded: chain S residue 265 CYS Chi-restraints excluded: chain S residue 272 VAL Chi-restraints excluded: chain S residue 287 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 170 GLN S 171 ASN ** S 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14571 Z= 0.175 Angle : 0.582 7.392 20909 Z= 0.341 Chirality : 0.035 0.152 2351 Planarity : 0.005 0.058 1659 Dihedral : 29.984 172.426 4260 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.33 % Allowed : 22.52 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.27), residues: 961 helix: 2.00 (0.22), residues: 556 sheet: -1.57 (0.85), residues: 38 loop : -1.32 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP S 135 HIS 0.008 0.001 HIS D 79 PHE 0.029 0.001 PHE S 219 TYR 0.032 0.002 TYR H 80 ARG 0.007 0.000 ARG S 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 202 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.7899 (p0) cc_final: 0.7686 (p0) REVERT: F 84 MET cc_start: 0.5515 (mtm) cc_final: 0.5187 (mtm) REVERT: F 100 PHE cc_start: 0.7964 (m-80) cc_final: 0.7588 (m-10) REVERT: G 68 ASN cc_start: 0.7434 (t0) cc_final: 0.7218 (t0) REVERT: H 27 ARG cc_start: 0.8029 (mmm160) cc_final: 0.6393 (ptp-170) REVERT: H 68 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7250 (tm-30) outliers start: 19 outliers final: 9 residues processed: 211 average time/residue: 0.2786 time to fit residues: 82.8184 Evaluate side-chains 188 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 179 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain S residue 272 VAL Chi-restraints excluded: chain S residue 287 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14571 Z= 0.299 Angle : 0.658 8.346 20909 Z= 0.378 Chirality : 0.039 0.162 2351 Planarity : 0.005 0.055 1659 Dihedral : 30.212 178.025 4260 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.77 % Allowed : 21.66 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.27), residues: 961 helix: 1.66 (0.21), residues: 553 sheet: -1.40 (0.87), residues: 40 loop : -1.34 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 135 HIS 0.013 0.001 HIS B 75 PHE 0.034 0.002 PHE S 219 TYR 0.048 0.002 TYR H 80 ARG 0.006 0.001 ARG S 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 183 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 LEU cc_start: 0.8941 (tp) cc_final: 0.8576 (tt) REVERT: E 93 GLN cc_start: 0.6461 (mt0) cc_final: 0.6135 (mt0) REVERT: F 88 TYR cc_start: 0.7511 (m-10) cc_final: 0.7300 (m-80) REVERT: H 27 ARG cc_start: 0.8199 (mmm160) cc_final: 0.6464 (ptp-170) REVERT: H 68 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7345 (tm-30) outliers start: 39 outliers final: 31 residues processed: 203 average time/residue: 0.2818 time to fit residues: 80.2626 Evaluate side-chains 206 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain S residue 218 THR Chi-restraints excluded: chain S residue 259 HIS Chi-restraints excluded: chain S residue 272 VAL Chi-restraints excluded: chain S residue 287 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14571 Z= 0.288 Angle : 0.658 11.037 20909 Z= 0.376 Chirality : 0.039 0.162 2351 Planarity : 0.005 0.056 1659 Dihedral : 30.259 179.891 4260 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.65 % Allowed : 21.91 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.27), residues: 961 helix: 1.50 (0.21), residues: 559 sheet: -1.58 (0.86), residues: 40 loop : -1.38 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 135 HIS 0.012 0.001 HIS B 75 PHE 0.030 0.002 PHE S 219 TYR 0.042 0.002 TYR H 80 ARG 0.009 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 181 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8810 (tp-100) cc_final: 0.7919 (tm-30) REVERT: B 58 LEU cc_start: 0.8957 (tp) cc_final: 0.8553 (tt) REVERT: G 41 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6541 (mm-30) REVERT: H 27 ARG cc_start: 0.8173 (mmm160) cc_final: 0.6427 (ptp-170) REVERT: H 68 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7386 (tm-30) REVERT: S 223 MET cc_start: 0.6480 (ptp) cc_final: 0.6137 (ptp) REVERT: S 244 PHE cc_start: 0.5635 (m-80) cc_final: 0.4677 (m-80) outliers start: 38 outliers final: 32 residues processed: 203 average time/residue: 0.2807 time to fit residues: 80.1477 Evaluate side-chains 207 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 175 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain S residue 218 THR Chi-restraints excluded: chain S residue 259 HIS Chi-restraints excluded: chain S residue 272 VAL Chi-restraints excluded: chain S residue 287 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14571 Z= 0.221 Angle : 0.622 9.707 20909 Z= 0.358 Chirality : 0.037 0.150 2351 Planarity : 0.005 0.057 1659 Dihedral : 30.193 178.503 4260 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.79 % Allowed : 22.89 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 961 helix: 1.71 (0.22), residues: 556 sheet: -1.63 (0.84), residues: 40 loop : -1.26 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP S 135 HIS 0.010 0.001 HIS B 75 PHE 0.028 0.002 PHE S 219 TYR 0.043 0.002 TYR H 80 ARG 0.006 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 183 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8768 (tp-100) cc_final: 0.7908 (tm-30) REVERT: B 58 LEU cc_start: 0.8955 (tp) cc_final: 0.8644 (tt) REVERT: E 63 ARG cc_start: 0.8130 (mmm-85) cc_final: 0.7928 (mmm-85) REVERT: H 27 ARG cc_start: 0.8077 (mmm160) cc_final: 0.6316 (ptp-170) REVERT: H 48 ASP cc_start: 0.7469 (t0) cc_final: 0.7085 (p0) REVERT: H 68 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7339 (tm-30) REVERT: H 96 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7897 (ttp80) REVERT: S 223 MET cc_start: 0.6462 (ptp) cc_final: 0.6175 (ptp) REVERT: S 244 PHE cc_start: 0.5605 (m-80) cc_final: 0.4808 (m-80) outliers start: 31 outliers final: 27 residues processed: 197 average time/residue: 0.2777 time to fit residues: 77.1689 Evaluate side-chains 199 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 172 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain S residue 259 HIS Chi-restraints excluded: chain S residue 272 VAL Chi-restraints excluded: chain S residue 287 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 6.9990 chunk 102 optimal weight: 0.0970 chunk 109 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14571 Z= 0.272 Angle : 0.652 8.872 20909 Z= 0.373 Chirality : 0.038 0.153 2351 Planarity : 0.005 0.055 1659 Dihedral : 30.249 178.664 4260 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.28 % Allowed : 22.77 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.27), residues: 961 helix: 1.54 (0.22), residues: 557 sheet: -1.88 (0.82), residues: 40 loop : -1.30 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 135 HIS 0.009 0.002 HIS B 75 PHE 0.029 0.002 PHE S 219 TYR 0.048 0.002 TYR H 80 ARG 0.010 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 LEU cc_start: 0.8967 (tp) cc_final: 0.8595 (tt) REVERT: H 27 ARG cc_start: 0.8070 (mmm160) cc_final: 0.6291 (ptp-170) REVERT: H 48 ASP cc_start: 0.7451 (t0) cc_final: 0.7096 (p0) REVERT: H 68 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7319 (tm-30) REVERT: H 90 GLU cc_start: 0.7206 (mp0) cc_final: 0.6758 (mp0) REVERT: H 96 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7968 (ttp80) REVERT: S 244 PHE cc_start: 0.5708 (m-80) cc_final: 0.4842 (m-80) outliers start: 35 outliers final: 31 residues processed: 195 average time/residue: 0.2793 time to fit residues: 77.6626 Evaluate side-chains 203 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain S residue 272 VAL Chi-restraints excluded: chain S residue 287 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 111 optimal weight: 0.0370 chunk 96 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS G 38 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14571 Z= 0.199 Angle : 0.614 8.735 20909 Z= 0.354 Chirality : 0.036 0.149 2351 Planarity : 0.005 0.059 1659 Dihedral : 30.162 178.925 4260 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.06 % Allowed : 23.26 % Favored : 73.68 % 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: 0.73 (0.27), residues: 961 helix: 1.71 (0.22), residues: 556 sheet: -1.76 (0.84), residues: 40 loop : -1.20 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP S 135 HIS 0.009 0.001 HIS B 75 PHE 0.029 0.002 PHE S 219 TYR 0.045 0.002 TYR H 80 ARG 0.008 0.000 ARG F 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 190 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 LEU cc_start: 0.8926 (tp) cc_final: 0.8571 (tt) REVERT: E 90 MET cc_start: 0.7309 (tmm) cc_final: 0.6694 (tmm) REVERT: H 27 ARG cc_start: 0.8003 (mmm160) cc_final: 0.6212 (ptp-170) REVERT: H 48 ASP cc_start: 0.7345 (t0) cc_final: 0.7105 (p0) REVERT: H 68 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7325 (tm-30) REVERT: H 96 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7789 (ttp80) REVERT: S 223 MET cc_start: 0.6355 (ptp) cc_final: 0.5984 (ptp) REVERT: S 244 PHE cc_start: 0.5514 (m-80) cc_final: 0.4795 (m-80) outliers start: 25 outliers final: 25 residues processed: 201 average time/residue: 0.2878 time to fit residues: 81.6393 Evaluate side-chains 202 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain S residue 185 ILE Chi-restraints excluded: chain S residue 218 THR Chi-restraints excluded: chain S residue 272 VAL Chi-restraints excluded: chain S residue 287 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 99 optimal weight: 50.0000 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.131073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.101453 restraints weight = 30397.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.103661 restraints weight = 16918.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.105098 restraints weight = 11813.165| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14571 Z= 0.265 Angle : 0.646 6.559 20909 Z= 0.371 Chirality : 0.038 0.171 2351 Planarity : 0.005 0.058 1659 Dihedral : 30.245 177.324 4260 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.55 % Allowed : 23.26 % Favored : 73.19 % 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: 0.56 (0.27), residues: 961 helix: 1.56 (0.22), residues: 556 sheet: -1.83 (0.82), residues: 40 loop : -1.25 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 135 HIS 0.008 0.001 HIS B 75 PHE 0.030 0.002 PHE S 219 TYR 0.039 0.002 TYR H 80 ARG 0.004 0.001 ARG S 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2504.87 seconds wall clock time: 45 minutes 45.79 seconds (2745.79 seconds total)