Starting phenix.real_space_refine on Sun Aug 24 01:47:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hqy_34954/08_2025/8hqy_34954.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hqy_34954/08_2025/8hqy_34954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hqy_34954/08_2025/8hqy_34954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hqy_34954/08_2025/8hqy_34954.map" model { file = "/net/cci-nas-00/data/ceres_data/8hqy_34954/08_2025/8hqy_34954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hqy_34954/08_2025/8hqy_34954.cif" } resolution = 3.05 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 Anisotropic ADP refinement not supported. Converting 5090 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 272 5.49 5 S 12 5.16 5 C 6888 2.51 5 N 2298 2.21 5 O 2832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12302 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 707 Classifications: {'peptide': 91} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 87} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 707 Classifications: {'peptide': 91} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 87} Chain: "S" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "U" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 593 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "I" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2775 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Chain: "J" Number of atoms: 2801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2801 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Time building chain proxies: 2.32, per 1000 atoms: 0.19 Number of scatterers: 12302 At special positions: 0 Unit cell: (123.51, 102.03, 115.992, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 272 15.00 O 2832 8.00 N 2298 7.00 C 6888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 340.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1586 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 11 sheets defined 67.0% alpha, 4.2% beta 135 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.984A pdb=" N ARG A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.667A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.665A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.605A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.718A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.534A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.683A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.676A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.533A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 4.124A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.070A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.722A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.494A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.710A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.678A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.567A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG H 99 " --> pdb=" O GLN H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.749A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 34 removed outlier: 3.529A pdb=" N LYS U 33 " --> pdb=" O LYS U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.783A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.569A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.528A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.786A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.495A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'U' and resid 12 through 16 removed outlier: 3.566A pdb=" N LEU U 15 " --> pdb=" O ILE U 3 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU U 69 " --> pdb=" O LYS U 6 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 343 hydrogen bonds 670 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 2020 1.32 - 1.44: 4361 1.44 - 1.56: 6123 1.56 - 1.68: 542 1.68 - 1.80: 23 Bond restraints: 13069 Sorted by residual: bond pdb=" CB GLU D 113 " pdb=" CG GLU D 113 " ideal model delta sigma weight residual 1.520 1.431 0.089 3.00e-02 1.11e+03 8.86e+00 bond pdb=" CG1 ILE F 50 " pdb=" CD1 ILE F 50 " ideal model delta sigma weight residual 1.513 1.400 0.113 3.90e-02 6.57e+02 8.39e+00 bond pdb=" C HIS H 49 " pdb=" N PRO H 50 " ideal model delta sigma weight residual 1.334 1.311 0.023 8.40e-03 1.42e+04 7.48e+00 bond pdb=" CB ARG B 92 " pdb=" CG ARG B 92 " ideal model delta sigma weight residual 1.520 1.440 0.080 3.00e-02 1.11e+03 7.10e+00 bond pdb=" CG1 ILE B 50 " pdb=" CD1 ILE B 50 " ideal model delta sigma weight residual 1.513 1.416 0.097 3.90e-02 6.57e+02 6.20e+00 ... (remaining 13064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 18138 2.39 - 4.78: 616 4.78 - 7.17: 45 7.17 - 9.56: 11 9.56 - 11.95: 3 Bond angle restraints: 18813 Sorted by residual: angle pdb=" N ARG U 72 " pdb=" CA ARG U 72 " pdb=" C ARG U 72 " ideal model delta sigma weight residual 110.91 116.07 -5.16 1.17e+00 7.31e-01 1.94e+01 angle pdb=" C SER S 181 " pdb=" N ASP S 182 " pdb=" CA ASP S 182 " ideal model delta sigma weight residual 121.80 132.51 -10.71 2.44e+00 1.68e-01 1.93e+01 angle pdb=" N ILE U 23 " pdb=" CA ILE U 23 " pdb=" C ILE U 23 " ideal model delta sigma weight residual 112.96 108.79 4.17 1.00e+00 1.00e+00 1.74e+01 angle pdb=" C LEU U 69 " pdb=" N VAL U 70 " pdb=" CA VAL U 70 " ideal model delta sigma weight residual 121.97 114.98 6.99 1.80e+00 3.09e-01 1.51e+01 angle pdb=" N ASP S 182 " pdb=" CA ASP S 182 " pdb=" C ASP S 182 " ideal model delta sigma weight residual 109.81 118.16 -8.35 2.21e+00 2.05e-01 1.43e+01 ... (remaining 18808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.96: 5473 28.96 - 57.93: 1574 57.93 - 86.89: 119 86.89 - 115.85: 1 115.85 - 144.82: 3 Dihedral angle restraints: 7170 sinusoidal: 4714 harmonic: 2456 Sorted by residual: dihedral pdb=" CA ALA A 114 " pdb=" C ALA A 114 " pdb=" N LYS A 115 " pdb=" CA LYS A 115 " ideal model delta harmonic sigma weight residual 180.00 156.65 23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LEU U 71 " pdb=" C LEU U 71 " pdb=" N ARG U 72 " pdb=" CA ARG U 72 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA VAL U 70 " pdb=" C VAL U 70 " pdb=" N LEU U 71 " pdb=" CA LEU U 71 " ideal model delta harmonic sigma weight residual 180.00 -157.73 -22.27 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 7167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1548 0.061 - 0.122: 511 0.122 - 0.183: 79 0.183 - 0.244: 10 0.244 - 0.306: 1 Chirality restraints: 2149 Sorted by residual: chirality pdb=" CG LEU E 126 " pdb=" CB LEU E 126 " pdb=" CD1 LEU E 126 " pdb=" CD2 LEU E 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ASP S 182 " pdb=" N ASP S 182 " pdb=" C ASP S 182 " pdb=" CB ASP S 182 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2146 not shown) Planarity restraints: 1438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 25 " -0.021 2.00e-02 2.50e+03 1.82e-02 5.77e+00 pdb=" CG PHE G 25 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE G 25 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE G 25 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE G 25 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE G 25 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE G 25 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 25 " -0.018 2.00e-02 2.50e+03 1.75e-02 5.38e+00 pdb=" CG PHE C 25 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE C 25 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 25 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 25 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 25 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 25 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 113 " -0.015 2.00e-02 2.50e+03 1.74e-02 4.53e+00 pdb=" CG HIS A 113 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS A 113 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS A 113 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 113 " 0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS A 113 " -0.010 2.00e-02 2.50e+03 ... (remaining 1435 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2351 2.77 - 3.30: 10282 3.30 - 3.84: 24690 3.84 - 4.37: 28483 4.37 - 4.90: 40595 Nonbonded interactions: 106401 Sorted by model distance: nonbonded pdb=" O2 DC I 116 " pdb=" N2 DG J 32 " model vdw 2.238 2.496 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.264 3.040 nonbonded pdb=" N2 DG I 126 " pdb=" O2 DC J 22 " model vdw 2.274 2.496 nonbonded pdb=" O HIS D 109 " pdb=" OG SER D 112 " model vdw 2.288 3.040 nonbonded pdb=" OE1 GLN A 68 " pdb=" NH1 ARG A 72 " model vdw 2.291 3.120 ... (remaining 106396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 13 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.330 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 : 0.011 0.113 13069 Z= 0.494 Angle : 1.013 11.952 18813 Z= 0.579 Chirality : 0.059 0.306 2149 Planarity : 0.007 0.052 1438 Dihedral : 27.346 144.817 5584 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.14 % Allowed : 3.24 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: -3.02 (0.24), residues: 828 helix: -1.68 (0.18), residues: 551 sheet: -3.05 (0.99), residues: 20 loop : -2.24 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 116 TYR 0.021 0.003 TYR F 98 PHE 0.040 0.005 PHE C 25 TRP 0.005 0.002 TRP S 164 HIS 0.020 0.004 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.01134 (13069) covalent geometry : angle 1.01264 (18813) hydrogen bonds : bond 0.11152 ( 746) hydrogen bonds : angle 4.17515 ( 1855) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 306 time to evaluate : 0.332 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: B 59 LYS cc_start: 0.9107 (tptt) cc_final: 0.8691 (tptp) REVERT: B 88 TYR cc_start: 0.8837 (m-10) cc_final: 0.8138 (m-10) REVERT: C 104 GLN cc_start: 0.8399 (mm110) cc_final: 0.8064 (mm-40) REVERT: D 105 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7819 (tp30) REVERT: E 41 TYR cc_start: 0.8368 (m-80) cc_final: 0.8007 (m-10) REVERT: F 59 LYS cc_start: 0.9203 (tptm) cc_final: 0.8663 (mmmm) REVERT: F 88 TYR cc_start: 0.8962 (m-10) cc_final: 0.8478 (m-80) REVERT: G 15 LYS cc_start: 0.8776 (ttmm) cc_final: 0.8382 (tmmt) REVERT: G 112 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8856 (mm110) REVERT: H 59 MET cc_start: 0.8941 (tpp) cc_final: 0.8616 (tpp) REVERT: H 83 TYR cc_start: 0.8318 (m-10) cc_final: 0.7991 (m-10) REVERT: U 48 LYS cc_start: 0.8553 (pttt) cc_final: 0.8178 (pttp) REVERT: U 50 LEU cc_start: 0.7793 (mm) cc_final: 0.7516 (mm) REVERT: U 63 LYS cc_start: 0.7992 (mttt) cc_final: 0.7710 (mtpp) REVERT: U 68 HIS cc_start: 0.8526 (m-70) cc_final: 0.8247 (m90) outliers start: 1 outliers final: 1 residues processed: 307 average time/residue: 0.1502 time to fit residues: 59.5168 Evaluate side-chains 218 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN C 104 GLN D 47 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 49 GLN U 68 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.060622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.039260 restraints weight = 53971.023| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.49 r_work: 0.2627 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13069 Z= 0.165 Angle : 0.641 11.949 18813 Z= 0.379 Chirality : 0.038 0.241 2149 Planarity : 0.005 0.048 1438 Dihedral : 30.863 147.829 3909 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.96 % Allowed : 10.72 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: -0.58 (0.29), residues: 828 helix: 0.38 (0.21), residues: 553 sheet: -2.40 (1.07), residues: 19 loop : -1.81 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 23 TYR 0.030 0.001 TYR D 83 PHE 0.014 0.001 PHE E 67 TRP 0.003 0.001 TRP S 164 HIS 0.003 0.001 HIS U 68 Details of bonding type rmsd covalent geometry : bond 0.00356 (13069) covalent geometry : angle 0.64130 (18813) hydrogen bonds : bond 0.05527 ( 746) hydrogen bonds : angle 3.12233 ( 1855) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 268 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8993 (mt-10) REVERT: A 59 GLU cc_start: 0.9080 (pm20) cc_final: 0.8781 (pm20) REVERT: A 68 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8766 (tm-30) REVERT: A 106 ASP cc_start: 0.8735 (m-30) cc_final: 0.8348 (m-30) REVERT: C 38 ASN cc_start: 0.8914 (m-40) cc_final: 0.8688 (m-40) REVERT: C 57 TYR cc_start: 0.9435 (t80) cc_final: 0.9207 (t80) REVERT: E 41 TYR cc_start: 0.8531 (m-80) cc_final: 0.8221 (m-10) REVERT: E 93 GLN cc_start: 0.9017 (tp40) cc_final: 0.8558 (tp40) REVERT: F 25 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8322 (m-40) REVERT: G 15 LYS cc_start: 0.8707 (ttmm) cc_final: 0.8270 (tmmt) REVERT: G 38 ASN cc_start: 0.8963 (m-40) cc_final: 0.8731 (m-40) REVERT: G 56 GLU cc_start: 0.8873 (tt0) cc_final: 0.8454 (mt-10) REVERT: G 89 ASN cc_start: 0.9046 (m110) cc_final: 0.8474 (m110) REVERT: G 92 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8470 (mt-10) REVERT: G 112 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8635 (mm110) REVERT: H 59 MET cc_start: 0.9272 (tpp) cc_final: 0.8963 (tpp) REVERT: H 83 TYR cc_start: 0.8510 (m-10) cc_final: 0.8167 (m-10) REVERT: H 93 GLU cc_start: 0.8967 (mp0) cc_final: 0.8643 (mp0) REVERT: S 167 ARG cc_start: 0.8733 (mtp180) cc_final: 0.8215 (mtm-85) REVERT: U 13 ILE cc_start: 0.9335 (mm) cc_final: 0.8905 (mm) REVERT: U 15 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8323 (pp) REVERT: U 48 LYS cc_start: 0.8448 (pttt) cc_final: 0.8096 (pttp) REVERT: U 63 LYS cc_start: 0.7533 (mttt) cc_final: 0.7316 (mtpp) outliers start: 21 outliers final: 8 residues processed: 278 average time/residue: 0.1122 time to fit residues: 42.9601 Evaluate side-chains 254 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 243 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 79 optimal weight: 1.9990 chunk 2 optimal weight: 0.0470 chunk 93 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 94 ASN C 112 GLN D 47 GLN D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN U 40 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.060576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.039198 restraints weight = 54615.341| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.53 r_work: 0.2622 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13069 Z= 0.168 Angle : 0.601 7.321 18813 Z= 0.358 Chirality : 0.037 0.176 2149 Planarity : 0.004 0.047 1438 Dihedral : 30.501 148.824 3908 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.82 % Allowed : 13.96 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 0.60 (0.30), residues: 828 helix: 1.38 (0.22), residues: 552 sheet: -1.65 (1.07), residues: 19 loop : -1.62 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 20 TYR 0.018 0.001 TYR D 83 PHE 0.012 0.001 PHE D 65 TRP 0.003 0.001 TRP S 164 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00367 (13069) covalent geometry : angle 0.60121 (18813) hydrogen bonds : bond 0.05147 ( 746) hydrogen bonds : angle 2.91763 ( 1855) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 251 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8979 (mt-10) REVERT: A 68 GLN cc_start: 0.8990 (tm130) cc_final: 0.8553 (tm-30) REVERT: A 80 THR cc_start: 0.9416 (p) cc_final: 0.9202 (p) REVERT: A 106 ASP cc_start: 0.8596 (m-30) cc_final: 0.8130 (m-30) REVERT: B 44 LYS cc_start: 0.9304 (mtpt) cc_final: 0.8954 (mtpt) REVERT: B 63 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8649 (mt-10) REVERT: C 57 TYR cc_start: 0.9411 (t80) cc_final: 0.9133 (t80) REVERT: C 64 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8798 (tm-30) REVERT: D 37 TYR cc_start: 0.9432 (m-80) cc_final: 0.9222 (m-80) REVERT: E 41 TYR cc_start: 0.8544 (m-80) cc_final: 0.8206 (m-10) REVERT: E 79 LYS cc_start: 0.8889 (tptp) cc_final: 0.8585 (tptp) REVERT: E 93 GLN cc_start: 0.9047 (tp40) cc_final: 0.8710 (tp40) REVERT: F 25 ASN cc_start: 0.9147 (OUTLIER) cc_final: 0.8169 (m-40) REVERT: G 15 LYS cc_start: 0.8671 (ttmm) cc_final: 0.8238 (tmmt) REVERT: G 36 LYS cc_start: 0.9270 (mmtp) cc_final: 0.9052 (mmtm) REVERT: G 56 GLU cc_start: 0.8871 (tt0) cc_final: 0.8447 (mt-10) REVERT: G 89 ASN cc_start: 0.9160 (m110) cc_final: 0.8635 (m110) REVERT: G 92 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8525 (mt-10) REVERT: G 112 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8498 (mm110) REVERT: H 93 GLU cc_start: 0.9012 (mp0) cc_final: 0.8626 (mp0) REVERT: U 6 LYS cc_start: 0.9203 (ttmt) cc_final: 0.8970 (ttmt) REVERT: U 13 ILE cc_start: 0.9270 (mm) cc_final: 0.8936 (mm) REVERT: U 15 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8441 (pp) REVERT: U 29 LYS cc_start: 0.9008 (mmmm) cc_final: 0.8712 (mptt) REVERT: U 50 LEU cc_start: 0.8597 (mm) cc_final: 0.7941 (mm) outliers start: 20 outliers final: 8 residues processed: 259 average time/residue: 0.1165 time to fit residues: 41.8088 Evaluate side-chains 248 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 238 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 29 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 53 optimal weight: 0.0870 chunk 47 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN D 47 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.060666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.039529 restraints weight = 54537.498| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.49 r_work: 0.2637 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13069 Z= 0.160 Angle : 0.590 7.280 18813 Z= 0.349 Chirality : 0.036 0.157 2149 Planarity : 0.004 0.048 1438 Dihedral : 30.301 147.869 3908 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.67 % Allowed : 15.09 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 1.19 (0.30), residues: 828 helix: 1.88 (0.22), residues: 552 sheet: -1.54 (1.06), residues: 19 loop : -1.51 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 32 TYR 0.013 0.001 TYR D 83 PHE 0.013 0.001 PHE D 65 TRP 0.004 0.001 TRP S 164 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00351 (13069) covalent geometry : angle 0.58964 (18813) hydrogen bonds : bond 0.04970 ( 746) hydrogen bonds : angle 2.85638 ( 1855) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8943 (mt-10) REVERT: A 94 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8745 (mt-10) REVERT: A 106 ASP cc_start: 0.8525 (m-30) cc_final: 0.8234 (m-30) REVERT: B 44 LYS cc_start: 0.9324 (mtpt) cc_final: 0.9123 (mtpp) REVERT: C 64 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8786 (tm-30) REVERT: D 68 ASP cc_start: 0.9231 (t70) cc_final: 0.8887 (t0) REVERT: E 41 TYR cc_start: 0.8533 (m-80) cc_final: 0.8201 (m-10) REVERT: E 93 GLN cc_start: 0.9198 (tp40) cc_final: 0.8724 (tp40) REVERT: F 25 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8651 (t0) REVERT: F 88 TYR cc_start: 0.9217 (m-10) cc_final: 0.8750 (m-10) REVERT: G 15 LYS cc_start: 0.8751 (ttmm) cc_final: 0.8290 (tmmt) REVERT: G 36 LYS cc_start: 0.9229 (mmtp) cc_final: 0.9009 (mmtm) REVERT: G 56 GLU cc_start: 0.8890 (tt0) cc_final: 0.8457 (mt-10) REVERT: G 89 ASN cc_start: 0.9167 (m110) cc_final: 0.8673 (m110) REVERT: G 92 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8546 (mt-10) REVERT: H 83 TYR cc_start: 0.8571 (m-10) cc_final: 0.8136 (m-10) REVERT: H 93 GLU cc_start: 0.9004 (mp0) cc_final: 0.8640 (mp0) REVERT: H 105 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8128 (tp30) REVERT: S 175 VAL cc_start: 0.9089 (t) cc_final: 0.8673 (p) REVERT: U 13 ILE cc_start: 0.9253 (mm) cc_final: 0.8949 (mm) REVERT: U 15 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8606 (pp) REVERT: U 29 LYS cc_start: 0.9011 (mmmm) cc_final: 0.8743 (mptt) REVERT: U 64 GLU cc_start: 0.7887 (mp0) cc_final: 0.7574 (mp0) outliers start: 26 outliers final: 8 residues processed: 258 average time/residue: 0.1128 time to fit residues: 40.4465 Evaluate side-chains 243 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 233 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN D 47 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.059834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.038768 restraints weight = 53926.405| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.42 r_work: 0.2602 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13069 Z= 0.209 Angle : 0.622 9.046 18813 Z= 0.364 Chirality : 0.037 0.174 2149 Planarity : 0.004 0.068 1438 Dihedral : 30.370 147.879 3908 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.53 % Allowed : 16.93 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 1.35 (0.30), residues: 828 helix: 2.03 (0.22), residues: 553 sheet: -1.54 (1.10), residues: 19 loop : -1.53 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 72 TYR 0.022 0.001 TYR C 57 PHE 0.013 0.001 PHE D 65 TRP 0.005 0.002 TRP S 164 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00469 (13069) covalent geometry : angle 0.62246 (18813) hydrogen bonds : bond 0.05175 ( 746) hydrogen bonds : angle 2.92763 ( 1855) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9309 (mt-10) cc_final: 0.8966 (mt-10) REVERT: A 94 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8768 (mt-10) REVERT: B 44 LYS cc_start: 0.9468 (mtpt) cc_final: 0.9246 (mtpp) REVERT: B 53 GLU cc_start: 0.8958 (tp30) cc_final: 0.8745 (tp30) REVERT: C 64 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8906 (tm-30) REVERT: D 46 LYS cc_start: 0.9342 (mmmt) cc_final: 0.9139 (mmmt) REVERT: D 68 ASP cc_start: 0.9259 (t70) cc_final: 0.8860 (t0) REVERT: E 41 TYR cc_start: 0.8573 (m-80) cc_final: 0.8239 (m-10) REVERT: E 93 GLN cc_start: 0.9229 (tp40) cc_final: 0.8727 (tp40) REVERT: F 25 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8667 (t0) REVERT: G 15 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8271 (tmmt) REVERT: G 89 ASN cc_start: 0.9254 (m110) cc_final: 0.8785 (m110) REVERT: G 92 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8503 (mt-10) REVERT: H 83 TYR cc_start: 0.8589 (m-10) cc_final: 0.8189 (m-10) REVERT: H 93 GLU cc_start: 0.9033 (mp0) cc_final: 0.8623 (mp0) REVERT: H 105 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8235 (tp30) REVERT: S 175 VAL cc_start: 0.9213 (t) cc_final: 0.8866 (p) REVERT: U 13 ILE cc_start: 0.9239 (mm) cc_final: 0.8972 (mm) REVERT: U 15 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8531 (pp) REVERT: U 49 GLN cc_start: 0.8642 (tt0) cc_final: 0.8286 (tp-100) outliers start: 25 outliers final: 18 residues processed: 241 average time/residue: 0.1034 time to fit residues: 34.5354 Evaluate side-chains 238 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 40 GLN Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 47 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.060798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.039847 restraints weight = 54061.502| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.44 r_work: 0.2639 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13069 Z= 0.156 Angle : 0.599 7.134 18813 Z= 0.353 Chirality : 0.036 0.157 2149 Planarity : 0.004 0.049 1438 Dihedral : 30.246 147.053 3908 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.24 % Allowed : 18.05 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 1.55 (0.30), residues: 828 helix: 2.15 (0.22), residues: 556 sheet: -1.75 (1.06), residues: 19 loop : -1.40 (0.42), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 42 TYR 0.021 0.001 TYR C 57 PHE 0.017 0.001 PHE D 65 TRP 0.003 0.001 TRP S 164 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00343 (13069) covalent geometry : angle 0.59938 (18813) hydrogen bonds : bond 0.04947 ( 746) hydrogen bonds : angle 2.83774 ( 1855) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 237 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8966 (mt-10) REVERT: A 94 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8730 (mt-10) REVERT: A 106 ASP cc_start: 0.8521 (m-30) cc_final: 0.8233 (m-30) REVERT: B 44 LYS cc_start: 0.9402 (mtpt) cc_final: 0.9187 (mtpp) REVERT: B 53 GLU cc_start: 0.8841 (tp30) cc_final: 0.8616 (tp30) REVERT: C 64 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8911 (tm-30) REVERT: D 68 ASP cc_start: 0.9214 (t70) cc_final: 0.8845 (t0) REVERT: E 41 TYR cc_start: 0.8544 (m-80) cc_final: 0.8168 (m-10) REVERT: E 93 GLN cc_start: 0.9208 (tp40) cc_final: 0.8675 (tp40) REVERT: F 25 ASN cc_start: 0.9043 (OUTLIER) cc_final: 0.8633 (t0) REVERT: G 15 LYS cc_start: 0.8712 (ttmm) cc_final: 0.8191 (tmmt) REVERT: G 36 LYS cc_start: 0.9188 (mmtp) cc_final: 0.8971 (mmtm) REVERT: G 56 GLU cc_start: 0.8956 (tt0) cc_final: 0.8605 (mt-10) REVERT: G 89 ASN cc_start: 0.9149 (m110) cc_final: 0.8687 (m-40) REVERT: G 92 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8569 (mt-10) REVERT: H 83 TYR cc_start: 0.8467 (m-10) cc_final: 0.8241 (m-10) REVERT: H 93 GLU cc_start: 0.9012 (mp0) cc_final: 0.8625 (mp0) REVERT: H 105 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8172 (tp30) REVERT: U 11 LYS cc_start: 0.9201 (ttpp) cc_final: 0.8903 (ttpt) REVERT: U 13 ILE cc_start: 0.9249 (mm) cc_final: 0.8534 (mm) REVERT: U 15 LEU cc_start: 0.8856 (pp) cc_final: 0.8532 (pp) REVERT: U 49 GLN cc_start: 0.8551 (tt0) cc_final: 0.8173 (tp-100) outliers start: 23 outliers final: 10 residues processed: 246 average time/residue: 0.1100 time to fit residues: 37.4822 Evaluate side-chains 237 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 226 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 43 LEU Chi-restraints excluded: chain U residue 50 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 78 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.060149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.039064 restraints weight = 53391.100| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.43 r_work: 0.2612 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13069 Z= 0.198 Angle : 0.621 6.957 18813 Z= 0.363 Chirality : 0.037 0.167 2149 Planarity : 0.004 0.050 1438 Dihedral : 30.334 146.788 3908 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.96 % Allowed : 19.46 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 1.59 (0.31), residues: 828 helix: 2.18 (0.22), residues: 556 sheet: -1.94 (1.03), residues: 19 loop : -1.34 (0.42), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 86 TYR 0.022 0.001 TYR C 57 PHE 0.015 0.001 PHE D 65 TRP 0.004 0.002 TRP S 164 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00446 (13069) covalent geometry : angle 0.62139 (18813) hydrogen bonds : bond 0.05088 ( 746) hydrogen bonds : angle 2.91913 ( 1855) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 227 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8970 (mt-10) REVERT: A 94 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8725 (mt-10) REVERT: A 106 ASP cc_start: 0.8513 (m-30) cc_final: 0.8296 (m-30) REVERT: B 53 GLU cc_start: 0.8909 (tp30) cc_final: 0.8654 (tp30) REVERT: C 64 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8956 (tm-30) REVERT: D 46 LYS cc_start: 0.9319 (mmmt) cc_final: 0.9064 (mmmt) REVERT: D 68 ASP cc_start: 0.9246 (t70) cc_final: 0.8868 (t0) REVERT: E 41 TYR cc_start: 0.8572 (m-80) cc_final: 0.8195 (m-10) REVERT: E 93 GLN cc_start: 0.9233 (tp40) cc_final: 0.8707 (tp40) REVERT: F 25 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8672 (t0) REVERT: G 15 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8182 (tmmt) REVERT: G 56 GLU cc_start: 0.8969 (tt0) cc_final: 0.8583 (mt-10) REVERT: G 89 ASN cc_start: 0.9229 (m110) cc_final: 0.8805 (m-40) REVERT: G 92 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8578 (mt-10) REVERT: H 93 GLU cc_start: 0.9048 (mp0) cc_final: 0.8616 (mp0) REVERT: H 105 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8254 (tp30) REVERT: S 175 VAL cc_start: 0.9004 (t) cc_final: 0.8653 (p) REVERT: U 6 LYS cc_start: 0.9155 (ttmt) cc_final: 0.8643 (mmtp) REVERT: U 11 LYS cc_start: 0.9250 (ttpp) cc_final: 0.8976 (ttpt) REVERT: U 13 ILE cc_start: 0.9286 (mm) cc_final: 0.8547 (mm) REVERT: U 15 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8522 (pp) REVERT: U 49 GLN cc_start: 0.8484 (tt0) cc_final: 0.8093 (tp-100) outliers start: 21 outliers final: 12 residues processed: 237 average time/residue: 0.1166 time to fit residues: 37.5996 Evaluate side-chains 235 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 221 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 17 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 74 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 GLN U 68 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.059672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.038260 restraints weight = 54213.744| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.45 r_work: 0.2587 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13069 Z= 0.221 Angle : 0.646 7.658 18813 Z= 0.375 Chirality : 0.038 0.175 2149 Planarity : 0.004 0.048 1438 Dihedral : 30.417 146.142 3908 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.81 % Allowed : 18.48 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 1.56 (0.31), residues: 828 helix: 2.14 (0.22), residues: 556 sheet: -1.97 (1.02), residues: 19 loop : -1.30 (0.42), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.025 0.002 TYR C 57 PHE 0.015 0.001 PHE D 65 TRP 0.004 0.002 TRP S 164 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00499 (13069) covalent geometry : angle 0.64644 (18813) hydrogen bonds : bond 0.05257 ( 746) hydrogen bonds : angle 2.99604 ( 1855) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9309 (mt-10) cc_final: 0.8957 (mt-10) REVERT: A 94 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8753 (mt-10) REVERT: B 53 GLU cc_start: 0.8954 (tp30) cc_final: 0.8702 (tp30) REVERT: C 64 GLU cc_start: 0.9237 (tm-30) cc_final: 0.9020 (tm-30) REVERT: D 46 LYS cc_start: 0.9311 (mmmt) cc_final: 0.9055 (mmmt) REVERT: D 68 ASP cc_start: 0.9280 (t70) cc_final: 0.8875 (t0) REVERT: E 41 TYR cc_start: 0.8647 (m-80) cc_final: 0.8277 (m-10) REVERT: E 93 GLN cc_start: 0.9271 (tp40) cc_final: 0.8691 (tp40) REVERT: F 25 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8517 (m-40) REVERT: G 15 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8159 (tmmt) REVERT: G 56 GLU cc_start: 0.8962 (tt0) cc_final: 0.8567 (mt-10) REVERT: G 89 ASN cc_start: 0.9320 (m110) cc_final: 0.8865 (m110) REVERT: G 92 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8523 (mt-10) REVERT: H 71 GLU cc_start: 0.9033 (tp30) cc_final: 0.8814 (tp30) REVERT: H 83 TYR cc_start: 0.8465 (m-10) cc_final: 0.8179 (m-10) REVERT: H 93 GLU cc_start: 0.9082 (mp0) cc_final: 0.8612 (mp0) REVERT: H 105 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8299 (tp30) REVERT: S 175 VAL cc_start: 0.9157 (t) cc_final: 0.8924 (p) REVERT: U 6 LYS cc_start: 0.9159 (ttmt) cc_final: 0.8664 (mmtp) REVERT: U 11 LYS cc_start: 0.9302 (ttpp) cc_final: 0.9017 (ttpt) REVERT: U 13 ILE cc_start: 0.9205 (mm) cc_final: 0.8485 (mm) REVERT: U 64 GLU cc_start: 0.7942 (mp0) cc_final: 0.7726 (mp0) REVERT: U 68 HIS cc_start: 0.8437 (m-70) cc_final: 0.8063 (m90) outliers start: 27 outliers final: 17 residues processed: 244 average time/residue: 0.1128 time to fit residues: 37.8213 Evaluate side-chains 239 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 221 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 25 ASN Chi-restraints excluded: chain U residue 40 GLN Chi-restraints excluded: chain U residue 60 ASN Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 42 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.060327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.039249 restraints weight = 53483.658| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.45 r_work: 0.2618 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13069 Z= 0.175 Angle : 0.632 6.978 18813 Z= 0.366 Chirality : 0.036 0.164 2149 Planarity : 0.004 0.050 1438 Dihedral : 30.292 145.427 3908 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.40 % Allowed : 19.75 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 1.68 (0.31), residues: 828 helix: 2.18 (0.22), residues: 557 sheet: -1.81 (1.07), residues: 19 loop : -1.15 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 42 TYR 0.024 0.002 TYR C 57 PHE 0.018 0.001 PHE D 65 TRP 0.004 0.001 TRP S 164 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00391 (13069) covalent geometry : angle 0.63160 (18813) hydrogen bonds : bond 0.05026 ( 746) hydrogen bonds : angle 2.93194 ( 1855) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 231 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8957 (mt-10) REVERT: A 94 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8711 (mt-10) REVERT: B 53 GLU cc_start: 0.8859 (tp30) cc_final: 0.8588 (tp30) REVERT: C 64 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8960 (tm-30) REVERT: C 89 ASN cc_start: 0.9408 (m-40) cc_final: 0.8976 (m110) REVERT: D 46 LYS cc_start: 0.9229 (mmmt) cc_final: 0.8970 (mmmt) REVERT: D 68 ASP cc_start: 0.9242 (t70) cc_final: 0.8831 (t0) REVERT: E 41 TYR cc_start: 0.8615 (m-80) cc_final: 0.8253 (m-10) REVERT: E 93 GLN cc_start: 0.9229 (tp40) cc_final: 0.8690 (tp40) REVERT: F 25 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8518 (m-40) REVERT: G 15 LYS cc_start: 0.8723 (ttmm) cc_final: 0.8165 (tmmt) REVERT: G 56 GLU cc_start: 0.8963 (tt0) cc_final: 0.8549 (mt-10) REVERT: G 89 ASN cc_start: 0.9282 (m110) cc_final: 0.8879 (m-40) REVERT: G 92 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8596 (mt-10) REVERT: H 71 GLU cc_start: 0.9021 (tp30) cc_final: 0.8814 (tp30) REVERT: H 83 TYR cc_start: 0.8424 (m-10) cc_final: 0.8202 (m-10) REVERT: H 93 GLU cc_start: 0.9072 (mp0) cc_final: 0.8642 (mp0) REVERT: H 105 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8208 (tp30) REVERT: S 175 VAL cc_start: 0.9157 (t) cc_final: 0.8922 (p) REVERT: U 6 LYS cc_start: 0.9133 (ttmt) cc_final: 0.8638 (mmtp) REVERT: U 11 LYS cc_start: 0.9262 (ttpp) cc_final: 0.8971 (ttpt) REVERT: U 13 ILE cc_start: 0.9214 (mm) cc_final: 0.8509 (mm) REVERT: U 64 GLU cc_start: 0.7960 (mp0) cc_final: 0.7747 (mp0) REVERT: U 68 HIS cc_start: 0.8320 (m-70) cc_final: 0.7955 (m90) outliers start: 17 outliers final: 13 residues processed: 241 average time/residue: 0.1154 time to fit residues: 38.1675 Evaluate side-chains 240 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 30 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.059219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.038022 restraints weight = 53956.772| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.43 r_work: 0.2575 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 13069 Z= 0.248 Angle : 0.672 6.933 18813 Z= 0.385 Chirality : 0.039 0.180 2149 Planarity : 0.004 0.048 1438 Dihedral : 30.470 145.169 3908 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.26 % Allowed : 20.45 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 1.49 (0.30), residues: 828 helix: 2.05 (0.22), residues: 557 sheet: -2.01 (1.01), residues: 19 loop : -1.23 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.026 0.002 TYR C 57 PHE 0.015 0.002 PHE D 65 TRP 0.004 0.002 TRP S 164 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00561 (13069) covalent geometry : angle 0.67155 (18813) hydrogen bonds : bond 0.05406 ( 746) hydrogen bonds : angle 3.06630 ( 1855) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 222 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9288 (mt-10) cc_final: 0.8949 (mt-10) REVERT: A 94 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8737 (mt-10) REVERT: B 53 GLU cc_start: 0.8940 (tp30) cc_final: 0.8680 (tp30) REVERT: C 64 GLU cc_start: 0.9238 (tm-30) cc_final: 0.9022 (tm-30) REVERT: D 46 LYS cc_start: 0.9246 (mmmt) cc_final: 0.8992 (mmmt) REVERT: D 68 ASP cc_start: 0.9287 (t70) cc_final: 0.8922 (t0) REVERT: E 41 TYR cc_start: 0.8620 (m-80) cc_final: 0.8242 (m-10) REVERT: E 93 GLN cc_start: 0.9283 (tp40) cc_final: 0.8681 (tp40) REVERT: F 25 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8535 (m-40) REVERT: G 15 LYS cc_start: 0.8783 (ttmm) cc_final: 0.8194 (tmmt) REVERT: G 56 GLU cc_start: 0.8970 (tt0) cc_final: 0.8570 (mt-10) REVERT: G 92 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8519 (mt-10) REVERT: H 83 TYR cc_start: 0.8470 (m-10) cc_final: 0.8090 (m-10) REVERT: H 93 GLU cc_start: 0.9083 (mp0) cc_final: 0.8655 (mp0) REVERT: H 105 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8310 (tp30) REVERT: U 6 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8590 (mmtp) REVERT: U 11 LYS cc_start: 0.9298 (ttpp) cc_final: 0.9001 (ttpt) REVERT: U 13 ILE cc_start: 0.9190 (mm) cc_final: 0.8461 (mm) REVERT: U 50 LEU cc_start: 0.8762 (mm) cc_final: 0.8519 (mm) REVERT: U 64 GLU cc_start: 0.8003 (mp0) cc_final: 0.7780 (mp0) outliers start: 16 outliers final: 13 residues processed: 231 average time/residue: 0.1236 time to fit residues: 38.9628 Evaluate side-chains 233 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 6 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.061006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.040046 restraints weight = 53323.097| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.44 r_work: 0.2648 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13069 Z= 0.158 Angle : 0.624 7.382 18813 Z= 0.362 Chirality : 0.036 0.165 2149 Planarity : 0.004 0.049 1438 Dihedral : 30.131 145.572 3908 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.26 % Allowed : 20.45 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % 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 aren not related in a simple way. whole: 1.66 (0.30), residues: 828 helix: 2.13 (0.22), residues: 558 sheet: -1.89 (1.04), residues: 19 loop : -1.08 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.023 0.001 TYR C 57 PHE 0.020 0.001 PHE D 65 TRP 0.003 0.001 TRP S 164 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00352 (13069) covalent geometry : angle 0.62393 (18813) hydrogen bonds : bond 0.05012 ( 746) hydrogen bonds : angle 2.89258 ( 1855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3005.32 seconds wall clock time: 51 minutes 49.87 seconds (3109.87 seconds total)