Starting phenix.real_space_refine on Mon Jul 6 00:30:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j02_35881/07_2026/8j02_35881_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j02_35881/07_2026/8j02_35881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j02_35881/07_2026/8j02_35881_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j02_35881/07_2026/8j02_35881_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j02_35881/07_2026/8j02_35881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j02_35881/07_2026/8j02_35881.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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 P 12 5.49 5 S 88 5.16 5 C 10440 2.51 5 N 2684 2.21 5 O 2892 1.98 5 H 15244 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31360 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5641 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 5641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5641 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 5641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5641 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 5641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5641 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'P0T': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'P0T': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'P0T': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'P0T': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.47, per 1000 atoms: 0.17 Number of scatterers: 31360 At special positions: 0 Unit cell: (119.97, 119.97, 124.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 12 15.00 O 2892 8.00 N 2684 7.00 C 10440 6.00 H 15244 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 - 3.00 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: 3.08 Conformation dependent library (CDL) restraints added in 979.5 milliseconds 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 4 sheets defined 82.7% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 91 through 115 Processing helix chain 'A' and resid 118 through 148 removed outlier: 4.027A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 removed outlier: 3.699A pdb=" N ARG A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 184 Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 254 Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 287 through 349 removed outlier: 4.388A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) Proline residue: A 308 - end of helix Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 357 through 367 Processing helix chain 'A' and resid 536 through 559 Processing helix chain 'A' and resid 563 through 600 removed outlier: 3.554A pdb=" N VAL A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) Proline residue: A 597 - end of helix Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 91 through 115 Processing helix chain 'B' and resid 118 through 148 removed outlier: 4.027A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.699A pdb=" N ARG B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 184 Processing helix chain 'B' and resid 196 through 211 Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'B' and resid 228 through 254 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 287 through 349 removed outlier: 4.388A pdb=" N ILE B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) Proline residue: B 308 - end of helix Proline residue: B 335 - end of helix Processing helix chain 'B' and resid 357 through 367 Processing helix chain 'B' and resid 536 through 559 Processing helix chain 'B' and resid 563 through 600 removed outlier: 3.554A pdb=" N VAL B 567 " --> pdb=" O ASP B 563 " (cutoff:3.500A) Proline residue: B 597 - end of helix Processing helix chain 'C' and resid 7 through 21 Processing helix chain 'C' and resid 29 through 41 Processing helix chain 'C' and resid 45 through 57 Processing helix chain 'C' and resid 65 through 75 Processing helix chain 'C' and resid 76 through 81 removed outlier: 3.628A pdb=" N ASP C 81 " --> pdb=" O MET C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 94 Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 139 through 148 Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 91 through 115 Processing helix chain 'D' and resid 118 through 148 removed outlier: 4.027A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 165 removed outlier: 3.699A pdb=" N ARG D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 184 Processing helix chain 'D' and resid 196 through 211 Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 254 Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 287 through 349 removed outlier: 4.388A pdb=" N ILE D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) Proline residue: D 308 - end of helix Proline residue: D 335 - end of helix Processing helix chain 'D' and resid 357 through 367 Processing helix chain 'D' and resid 536 through 559 Processing helix chain 'D' and resid 563 through 600 removed outlier: 3.554A pdb=" N VAL D 567 " --> pdb=" O ASP D 563 " (cutoff:3.500A) Proline residue: D 597 - end of helix Processing helix chain 'E' and resid 7 through 21 Processing helix chain 'E' and resid 29 through 41 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 65 through 75 Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.628A pdb=" N ASP E 81 " --> pdb=" O MET E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 94 Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 139 through 148 Processing helix chain 'G' and resid 71 through 86 Processing helix chain 'G' and resid 91 through 115 Processing helix chain 'G' and resid 118 through 148 removed outlier: 4.027A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 165 removed outlier: 3.699A pdb=" N ARG G 160 " --> pdb=" O GLY G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 184 Processing helix chain 'G' and resid 196 through 211 Processing helix chain 'G' and resid 215 through 228 Processing helix chain 'G' and resid 228 through 254 Processing helix chain 'G' and resid 263 through 276 Processing helix chain 'G' and resid 287 through 349 removed outlier: 4.388A pdb=" N ILE G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) Proline residue: G 308 - end of helix Proline residue: G 335 - end of helix Processing helix chain 'G' and resid 357 through 367 Processing helix chain 'G' and resid 536 through 559 Processing helix chain 'G' and resid 563 through 600 removed outlier: 3.554A pdb=" N VAL G 567 " --> pdb=" O ASP G 563 " (cutoff:3.500A) Proline residue: G 597 - end of helix Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 76 through 81 removed outlier: 3.628A pdb=" N ASP H 81 " --> pdb=" O MET H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 94 Processing helix chain 'H' and resid 103 through 111 Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 139 through 148 Processing helix chain 'F' and resid 7 through 21 Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 65 through 75 Processing helix chain 'F' and resid 76 through 81 removed outlier: 3.628A pdb=" N ASP F 81 " --> pdb=" O MET F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 139 through 148 Processing sheet with id=AA1, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'H' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'F' and resid 100 through 102 1245 hydrogen bonds defined for protein. 3735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.21 Time building geometry restraints manager: 4.16 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: 15216 1.03 - 1.23: 40 1.23 - 1.42: 6956 1.42 - 1.62: 9308 1.62 - 1.81: 172 Bond restraints: 31692 Sorted by residual: bond pdb=" C07 P0T A 801 " pdb=" C09 P0T A 801 " ideal model delta sigma weight residual 1.336 1.594 -0.258 2.00e-02 2.50e+03 1.66e+02 bond pdb=" C07 P0T B 802 " pdb=" C09 P0T B 802 " ideal model delta sigma weight residual 1.336 1.593 -0.257 2.00e-02 2.50e+03 1.66e+02 bond pdb=" C07 P0T G 802 " pdb=" C09 P0T G 802 " ideal model delta sigma weight residual 1.336 1.593 -0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" C07 P0T D 802 " pdb=" C09 P0T D 802 " ideal model delta sigma weight residual 1.336 1.593 -0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" C10 P0T A 801 " pdb=" C19 P0T A 801 " ideal model delta sigma weight residual 1.331 1.552 -0.221 2.00e-02 2.50e+03 1.22e+02 ... (remaining 31687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.13: 56744 6.13 - 12.26: 64 12.26 - 18.39: 8 18.39 - 24.52: 8 24.52 - 30.65: 4 Bond angle restraints: 56828 Sorted by residual: angle pdb=" C07 P0T A 801 " pdb=" C04 P0T A 801 " pdb=" C08 P0T A 801 " ideal model delta sigma weight residual 112.03 81.38 30.65 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C07 P0T G 802 " pdb=" C04 P0T G 802 " pdb=" C08 P0T G 802 " ideal model delta sigma weight residual 112.03 81.38 30.65 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C07 P0T B 802 " pdb=" C04 P0T B 802 " pdb=" C08 P0T B 802 " ideal model delta sigma weight residual 112.03 81.43 30.60 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C07 P0T D 802 " pdb=" C04 P0T D 802 " pdb=" C08 P0T D 802 " ideal model delta sigma weight residual 112.03 81.44 30.59 3.00e+00 1.11e-01 1.04e+02 angle pdb=" O11 PIO D 801 " pdb=" P1 PIO D 801 " pdb=" O12 PIO D 801 " ideal model delta sigma weight residual 121.09 101.01 20.08 3.00e+00 1.11e-01 4.48e+01 ... (remaining 56823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.88: 13252 21.88 - 43.76: 1164 43.76 - 65.64: 328 65.64 - 87.52: 48 87.52 - 109.40: 12 Dihedral angle restraints: 14804 sinusoidal: 7928 harmonic: 6876 Sorted by residual: dihedral pdb=" C03 P0T G 802 " pdb=" C05 P0T G 802 " pdb=" C06 P0T G 802 " pdb=" C09 P0T G 802 " ideal model delta sinusoidal sigma weight residual 49.00 -60.40 109.40 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C03 P0T B 802 " pdb=" C05 P0T B 802 " pdb=" C06 P0T B 802 " pdb=" C09 P0T B 802 " ideal model delta sinusoidal sigma weight residual 49.00 -60.40 109.40 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C03 P0T D 802 " pdb=" C05 P0T D 802 " pdb=" C06 P0T D 802 " pdb=" C09 P0T D 802 " ideal model delta sinusoidal sigma weight residual 49.00 -60.39 109.39 1 3.00e+01 1.11e-03 1.42e+01 ... (remaining 14801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 1520 0.023 - 0.045: 564 0.045 - 0.068: 220 0.068 - 0.090: 108 0.090 - 0.113: 52 Chirality restraints: 2464 Sorted by residual: chirality pdb=" CA PRO B 167 " pdb=" N PRO B 167 " pdb=" C PRO B 167 " pdb=" CB PRO B 167 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.18e-01 chirality pdb=" CA PRO D 167 " pdb=" N PRO D 167 " pdb=" C PRO D 167 " pdb=" CB PRO D 167 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.18e-01 chirality pdb=" CA PRO A 167 " pdb=" N PRO A 167 " pdb=" C PRO A 167 " pdb=" CB PRO A 167 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.18e-01 ... (remaining 2461 not shown) Planarity restraints: 4700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 66 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO H 67 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO H 67 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 67 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 66 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO E 67 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 66 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO C 67 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 67 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 67 " 0.027 5.00e-02 4.00e+02 ... (remaining 4697 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 2892 2.21 - 2.81: 65839 2.81 - 3.41: 90439 3.41 - 4.00: 109584 4.00 - 4.60: 170949 Nonbonded interactions: 439703 Sorted by model distance: nonbonded pdb=" O VAL C 36 " pdb=" HG SER C 39 " model vdw 1.615 2.450 nonbonded pdb=" O VAL F 36 " pdb=" HG SER F 39 " model vdw 1.615 2.450 nonbonded pdb=" O VAL E 36 " pdb=" HG SER E 39 " model vdw 1.615 2.450 nonbonded pdb=" O VAL H 36 " pdb=" HG SER H 39 " model vdw 1.615 2.450 nonbonded pdb=" OE1 GLU E 120 " pdb=" H GLU E 120 " model vdw 1.633 2.450 ... (remaining 439698 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 70 through 600) selection = (chain 'B' and resid 70 through 600) selection = (chain 'D' and resid 70 through 600) selection = (chain 'G' and resid 70 through 600) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.190 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.700 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 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 : 0.009 0.258 16448 Z= 0.432 Angle : 1.015 30.650 22156 Z= 0.423 Chirality : 0.033 0.113 2464 Planarity : 0.003 0.048 2768 Dihedral : 18.341 109.399 5980 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.72 % Allowed : 24.16 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.19), residues: 1956 helix: 1.97 (0.13), residues: 1596 sheet: None (None), residues: 0 loop : -0.53 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.012 0.001 TYR A 362 PHE 0.028 0.001 PHE H 20 TRP 0.008 0.001 TRP B 344 HIS 0.001 0.000 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00864 / 0.43 (16448) covalent geometry : angle 1.01463 / 0.42 (22156) hydrogen bonds : bond 0.10382 / 6.87 ( 1245) hydrogen bonds : angle 5.19705 / 3.84 ( 3735) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 284 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 272 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 LEU cc_start: 0.8442 (mt) cc_final: 0.8176 (mp) REVERT: E 49 LEU cc_start: 0.8443 (mt) cc_final: 0.8177 (mp) REVERT: H 49 LEU cc_start: 0.8441 (mt) cc_final: 0.8175 (mp) REVERT: F 49 LEU cc_start: 0.8440 (mt) cc_final: 0.8172 (mp) outliers start: 12 outliers final: 8 residues processed: 276 average time/residue: 0.2606 time to fit residues: 110.6272 Evaluate side-chains 248 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 240 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain F residue 139 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 286 GLN A 570 GLN B 258 ASN B 286 GLN B 570 GLN D 258 ASN D 286 GLN D 570 GLN G 258 ASN G 286 GLN G 570 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.157446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.110868 restraints weight = 102146.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.114030 restraints weight = 47543.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.113886 restraints weight = 31406.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.114529 restraints weight = 30934.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.114532 restraints weight = 28851.565| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16448 Z= 0.155 Angle : 0.556 4.945 22156 Z= 0.308 Chirality : 0.034 0.125 2464 Planarity : 0.004 0.045 2768 Dihedral : 8.295 61.461 2280 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.57 % Allowed : 23.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.19), residues: 1956 helix: 2.00 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -0.41 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 87 TYR 0.010 0.001 TYR G 571 PHE 0.024 0.001 PHE C 20 TRP 0.008 0.001 TRP G 344 HIS 0.004 0.001 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (16448) covalent geometry : angle 0.55617 / 0.31 (22156) hydrogen bonds : bond 0.04932 / 3.39 ( 1245) hydrogen bonds : angle 4.57188 / 3.39 ( 3735) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 295 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 ASP cc_start: 0.8570 (t0) cc_final: 0.8342 (p0) REVERT: E 119 ASP cc_start: 0.8573 (t0) cc_final: 0.8347 (p0) REVERT: H 119 ASP cc_start: 0.8571 (t0) cc_final: 0.8344 (p0) REVERT: F 119 ASP cc_start: 0.8569 (t0) cc_final: 0.8342 (p0) outliers start: 43 outliers final: 27 residues processed: 283 average time/residue: 0.2613 time to fit residues: 111.7839 Evaluate side-chains 263 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 258 ASN Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 258 ASN Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain F residue 139 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 28 optimal weight: 30.0000 chunk 151 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 158 optimal weight: 0.7980 chunk 169 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.154677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.112401 restraints weight = 101496.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.112140 restraints weight = 45655.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.112026 restraints weight = 34040.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.112561 restraints weight = 32967.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.112608 restraints weight = 31051.639| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16448 Z= 0.244 Angle : 0.583 5.513 22156 Z= 0.334 Chirality : 0.036 0.141 2464 Planarity : 0.004 0.045 2768 Dihedral : 7.272 61.404 2278 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.07 % Allowed : 24.16 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.19), residues: 1956 helix: 1.78 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -0.72 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 87 TYR 0.011 0.001 TYR E 139 PHE 0.021 0.002 PHE C 20 TRP 0.007 0.001 TRP D 218 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.24 (16448) covalent geometry : angle 0.58293 / 0.33 (22156) hydrogen bonds : bond 0.05163 / 3.56 ( 1245) hydrogen bonds : angle 4.74228 / 3.52 ( 3735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 213 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 52 residues processed: 265 average time/residue: 0.2579 time to fit residues: 101.9051 Evaluate side-chains 253 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 201 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 157 TRP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 157 TRP Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 584 SER Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain F residue 141 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 48 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS B 228 HIS D 228 HIS G 228 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.157213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.109054 restraints weight = 100854.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 79)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.113649 restraints weight = 38295.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.116060 restraints weight = 25987.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.117035 restraints weight = 22565.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.117126 restraints weight = 21421.271| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16448 Z= 0.142 Angle : 0.505 4.540 22156 Z= 0.285 Chirality : 0.033 0.120 2464 Planarity : 0.003 0.043 2768 Dihedral : 6.631 58.797 2278 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.45 % Allowed : 24.34 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.19), residues: 1956 helix: 2.02 (0.13), residues: 1628 sheet: None (None), residues: 0 loop : -0.61 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 87 TYR 0.012 0.001 TYR E 139 PHE 0.022 0.001 PHE C 20 TRP 0.007 0.001 TRP A 288 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (16448) covalent geometry : angle 0.50460 / 0.29 (22156) hydrogen bonds : bond 0.04668 / 3.19 ( 1245) hydrogen bonds : angle 4.39483 / 3.26 ( 3735) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 33 residues processed: 253 average time/residue: 0.2624 time to fit residues: 101.0367 Evaluate side-chains 245 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 157 TRP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 157 TRP Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 584 SER Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain F residue 139 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 83 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.154757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.106122 restraints weight = 102293.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.110505 restraints weight = 39293.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.112805 restraints weight = 26774.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.113657 restraints weight = 23294.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.113903 restraints weight = 22159.892| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16448 Z= 0.203 Angle : 0.546 4.542 22156 Z= 0.312 Chirality : 0.034 0.135 2464 Planarity : 0.004 0.045 2768 Dihedral : 7.138 58.569 2272 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.87 % Allowed : 24.64 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.19), residues: 1956 helix: 1.95 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -0.66 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 87 TYR 0.012 0.001 TYR H 139 PHE 0.025 0.002 PHE C 20 TRP 0.009 0.001 TRP A 218 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 (16448) covalent geometry : angle 0.54551 / 0.31 (22156) hydrogen bonds : bond 0.04894 / 3.36 ( 1245) hydrogen bonds : angle 4.48475 / 3.33 ( 3735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 48 residues processed: 245 average time/residue: 0.2505 time to fit residues: 95.3663 Evaluate side-chains 261 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 157 TRP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 157 TRP Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 584 SER Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 87 ARG Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain F residue 146 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 chunk 172 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 341 GLN ** 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 = 0.4450 r_free = 0.4450 target = 0.158058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.113375 restraints weight = 105477.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.116842 restraints weight = 44852.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.116437 restraints weight = 30282.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.117538 restraints weight = 30586.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.116990 restraints weight = 27848.549| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16448 Z= 0.128 Angle : 0.500 4.584 22156 Z= 0.279 Chirality : 0.033 0.119 2464 Planarity : 0.003 0.044 2768 Dihedral : 6.379 56.108 2272 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.11 % Allowed : 23.68 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.19), residues: 1956 helix: 2.19 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -0.52 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.011 0.001 TYR H 139 PHE 0.029 0.001 PHE C 20 TRP 0.006 0.001 TRP B 288 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (16448) covalent geometry : angle 0.50001 / 0.28 (22156) hydrogen bonds : bond 0.04469 / 3.05 ( 1245) hydrogen bonds : angle 4.22053 / 3.14 ( 3735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 287 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 235 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 48 residues processed: 267 average time/residue: 0.2469 time to fit residues: 102.8944 Evaluate side-chains 275 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 157 TRP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 157 TRP Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 579 LEU Chi-restraints excluded: chain G residue 584 SER Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain F residue 146 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 40 optimal weight: 20.0000 chunk 123 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.154184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.110232 restraints weight = 102415.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.110639 restraints weight = 48530.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.110278 restraints weight = 34736.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.110769 restraints weight = 33944.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.110849 restraints weight = 32606.693| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16448 Z= 0.229 Angle : 0.571 4.455 22156 Z= 0.327 Chirality : 0.035 0.139 2464 Planarity : 0.004 0.045 2768 Dihedral : 6.919 57.251 2272 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.59 % Allowed : 24.16 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.19), residues: 1956 helix: 2.02 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -0.74 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 581 TYR 0.011 0.001 TYR H 139 PHE 0.026 0.002 PHE C 20 TRP 0.009 0.001 TRP D 218 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.23 (16448) covalent geometry : angle 0.57085 / 0.33 (22156) hydrogen bonds : bond 0.04942 / 3.41 ( 1245) hydrogen bonds : angle 4.47666 / 3.32 ( 3735) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 216 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 52 residues processed: 252 average time/residue: 0.2363 time to fit residues: 92.5456 Evaluate side-chains 272 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 220 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 157 TRP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 157 TRP Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 579 LEU Chi-restraints excluded: chain G residue 584 SER Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 87 ARG Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain F residue 146 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 87 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 154 optimal weight: 0.8980 chunk 185 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 189 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 341 GLN ** 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 = 0.4419 r_free = 0.4419 target = 0.155879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.109672 restraints weight = 106057.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.112679 restraints weight = 49839.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.112827 restraints weight = 32252.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.113854 restraints weight = 31953.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.113485 restraints weight = 29495.135| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16448 Z= 0.185 Angle : 0.546 4.505 22156 Z= 0.311 Chirality : 0.034 0.132 2464 Planarity : 0.003 0.044 2768 Dihedral : 6.792 57.988 2272 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.11 % Allowed : 25.96 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.19), residues: 1956 helix: 2.03 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : -0.74 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 87 TYR 0.011 0.001 TYR H 139 PHE 0.026 0.001 PHE C 20 TRP 0.007 0.001 TRP B 288 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (16448) covalent geometry : angle 0.54628 / 0.31 (22156) hydrogen bonds : bond 0.04798 / 3.30 ( 1245) hydrogen bonds : angle 4.39273 / 3.27 ( 3735) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 224 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.6627 (OUTLIER) cc_final: 0.6318 (t80) REVERT: B 93 PHE cc_start: 0.6633 (OUTLIER) cc_final: 0.6319 (t80) REVERT: D 93 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.6320 (t80) REVERT: G 93 PHE cc_start: 0.6635 (OUTLIER) cc_final: 0.6324 (t80) outliers start: 52 outliers final: 44 residues processed: 260 average time/residue: 0.2323 time to fit residues: 93.8015 Evaluate side-chains 264 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 157 TRP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 157 TRP Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 579 LEU Chi-restraints excluded: chain G residue 584 SER Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain F residue 146 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN B 341 GLN D 341 GLN G 341 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.156080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.110357 restraints weight = 105786.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.113406 restraints weight = 48143.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.113437 restraints weight = 31605.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.114474 restraints weight = 31525.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.114067 restraints weight = 29130.510| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16448 Z= 0.166 Angle : 0.545 4.982 22156 Z= 0.308 Chirality : 0.034 0.129 2464 Planarity : 0.003 0.044 2768 Dihedral : 6.668 57.482 2272 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.11 % Allowed : 26.14 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.19), residues: 1956 helix: 2.10 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -0.73 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 581 TYR 0.011 0.001 TYR E 139 PHE 0.030 0.001 PHE E 20 TRP 0.007 0.001 TRP G 288 HIS 0.003 0.001 HIS G 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (16448) covalent geometry : angle 0.54472 / 0.31 (22156) hydrogen bonds : bond 0.04680 / 3.21 ( 1245) hydrogen bonds : angle 4.33078 / 3.22 ( 3735) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 220 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.6567 (OUTLIER) cc_final: 0.6259 (t80) REVERT: B 93 PHE cc_start: 0.6573 (OUTLIER) cc_final: 0.6264 (t80) REVERT: D 93 PHE cc_start: 0.6573 (OUTLIER) cc_final: 0.6259 (t80) REVERT: G 93 PHE cc_start: 0.6575 (OUTLIER) cc_final: 0.6267 (t80) outliers start: 52 outliers final: 44 residues processed: 256 average time/residue: 0.2494 time to fit residues: 99.4174 Evaluate side-chains 272 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 157 TRP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 157 TRP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 157 TRP Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 579 LEU Chi-restraints excluded: chain G residue 584 SER Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain F residue 146 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 92 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 173 optimal weight: 0.2980 chunk 161 optimal weight: 30.0000 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 187 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN B 341 GLN D 341 GLN G 341 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.156401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.110613 restraints weight = 105596.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.113692 restraints weight = 48120.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.113699 restraints weight = 31544.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.114778 restraints weight = 31419.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.114374 restraints weight = 28987.697| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16448 Z= 0.160 Angle : 0.542 5.831 22156 Z= 0.307 Chirality : 0.034 0.128 2464 Planarity : 0.003 0.044 2768 Dihedral : 6.613 57.168 2272 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.87 % Allowed : 25.66 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.19), residues: 1956 helix: 2.12 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -0.74 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 332 TYR 0.011 0.001 TYR H 139 PHE 0.031 0.001 PHE H 20 TRP 0.007 0.001 TRP A 270 HIS 0.002 0.001 HIS G 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (16448) covalent geometry : angle 0.54244 / 0.31 (22156) hydrogen bonds : bond 0.04630 / 3.17 ( 1245) hydrogen bonds : angle 4.32044 / 3.22 ( 3735) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue THR 354 is missing expected H atoms. Skipping. Residue LEU 356 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue THR 359 is missing expected H atoms. Skipping. Residue TYR 362 is missing expected H atoms. Skipping. Residue TYR 363 is missing expected H atoms. Skipping. Residue THR 366 is missing expected H atoms. Skipping. Residue LYS 537 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.6607 (OUTLIER) cc_final: 0.6274 (t80) REVERT: B 93 PHE cc_start: 0.6609 (OUTLIER) cc_final: 0.6276 (t80) REVERT: D 93 PHE cc_start: 0.6610 (OUTLIER) cc_final: 0.6272 (t80) REVERT: G 93 PHE cc_start: 0.6612 (OUTLIER) cc_final: 0.6276 (t80) outliers start: 48 outliers final: 40 residues processed: 256 average time/residue: 0.2492 time to fit residues: 99.0067 Evaluate side-chains 264 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 220 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 584 SER Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 579 LEU Chi-restraints excluded: chain G residue 584 SER Chi-restraints excluded: chain G residue 589 VAL Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 139 TYR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain F residue 146 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 186 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN B 341 GLN D 341 GLN G 341 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.154757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.108543 restraints weight = 105871.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.111755 restraints weight = 43915.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.111569 restraints weight = 29080.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.111668 restraints weight = 30711.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.111964 restraints weight = 28635.459| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16448 Z= 0.216 Angle : 0.579 6.027 22156 Z= 0.331 Chirality : 0.035 0.138 2464 Planarity : 0.004 0.044 2768 Dihedral : 7.121 59.602 2272 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.87 % Allowed : 25.84 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.19), residues: 1956 helix: 1.94 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -0.78 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 541 TYR 0.011 0.001 TYR E 139 PHE 0.030 0.002 PHE C 20 TRP 0.008 0.001 TRP A 288 HIS 0.003 0.001 HIS D 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.22 (16448) covalent geometry : angle 0.57939 / 0.33 (22156) hydrogen bonds : bond 0.04915 / 3.38 ( 1245) hydrogen bonds : angle 4.47877 / 3.33 ( 3735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4976.06 seconds wall clock time: 85 minutes 37.57 seconds (5137.57 seconds total)