Starting phenix.real_space_refine on Sat Jun 14 11:48:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hqy_34954/06_2025/8hqy_34954.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hqy_34954/06_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_34954/06_2025/8hqy_34954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hqy_34954/06_2025/8hqy_34954.map" model { file = "/net/cci-nas-00/data/ceres_data/8hqy_34954/06_2025/8hqy_34954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hqy_34954/06_2025/8hqy_34954.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} 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: 7.56, per 1000 atoms: 0.61 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: 2.87 Conformation dependent library (CDL) restraints added in 995.3 milliseconds 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: 5.53 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: 4.39 Time building geometry restraints manager: 3.49 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.580 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.790 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.002 TRP S 164 HIS 0.020 0.004 HIS A 113 PHE 0.040 0.005 PHE C 25 TYR 0.021 0.003 TYR F 98 ARG 0.017 0.002 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.11152 ( 746) hydrogen bonds : angle 4.17515 ( 1855) covalent geometry : bond 0.01134 (13069) covalent geometry : angle 1.01264 (18813) *********************** 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 : 1.015 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: 0.3990 time to fit residues: 158.0489 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 : 2.029 ------------------------------------------------------------------------------- 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 90 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.059831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.038346 restraints weight = 54168.231| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.49 r_work: 0.2595 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 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 = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13069 Z= 0.206 Angle : 0.662 11.545 18813 Z= 0.389 Chirality : 0.039 0.237 2149 Planarity : 0.005 0.048 1438 Dihedral : 30.944 147.931 3909 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.53 % Allowed : 11.00 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.29), residues: 828 helix: 0.43 (0.21), residues: 553 sheet: -2.54 (1.04), residues: 19 loop : -1.80 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 164 HIS 0.004 0.001 HIS B 75 PHE 0.015 0.002 PHE E 67 TYR 0.031 0.001 TYR D 83 ARG 0.008 0.001 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.05653 ( 746) hydrogen bonds : angle 3.16769 ( 1855) covalent geometry : bond 0.00454 (13069) covalent geometry : angle 0.66215 (18813) *********************** 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 284 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 259 time to evaluate : 1.056 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: 0.9324 (mt-10) cc_final: 0.9000 (mt-10) REVERT: A 59 GLU cc_start: 0.9099 (pm20) cc_final: 0.8769 (pm20) REVERT: A 68 GLN cc_start: 0.9251 (OUTLIER) cc_final: 0.8990 (tm-30) REVERT: A 106 ASP cc_start: 0.8603 (m-30) cc_final: 0.8209 (m-30) REVERT: B 63 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8706 (mt-10) REVERT: C 57 TYR cc_start: 0.9472 (t80) cc_final: 0.9223 (t80) REVERT: C 89 ASN cc_start: 0.9443 (m-40) cc_final: 0.9199 (m-40) REVERT: C 92 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8124 (mt-10) REVERT: D 59 MET cc_start: 0.9309 (tpp) cc_final: 0.9090 (tpt) REVERT: E 41 TYR cc_start: 0.8583 (m-80) cc_final: 0.8281 (m-10) REVERT: E 93 GLN cc_start: 0.9079 (tp40) cc_final: 0.8600 (tp40) REVERT: F 25 ASN cc_start: 0.9180 (OUTLIER) cc_final: 0.8288 (m-40) REVERT: G 15 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8244 (tmmt) REVERT: G 38 ASN cc_start: 0.8954 (m-40) cc_final: 0.8740 (m-40) REVERT: G 56 GLU cc_start: 0.8920 (tt0) cc_final: 0.8482 (mt-10) REVERT: G 89 ASN cc_start: 0.9045 (m110) cc_final: 0.8476 (m110) REVERT: G 92 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8505 (mt-10) REVERT: G 112 GLN cc_start: 0.8929 (mm-40) cc_final: 0.8645 (mm110) REVERT: H 59 MET cc_start: 0.9278 (tpp) cc_final: 0.8991 (tpp) REVERT: H 76 GLU cc_start: 0.8885 (tp30) cc_final: 0.8670 (tp30) REVERT: H 83 TYR cc_start: 0.8534 (m-10) cc_final: 0.8212 (m-10) REVERT: H 93 GLU cc_start: 0.9008 (mp0) cc_final: 0.8654 (mp0) REVERT: S 167 ARG cc_start: 0.8755 (mtp180) cc_final: 0.8191 (mtm-85) REVERT: U 13 ILE cc_start: 0.9339 (mm) cc_final: 0.8905 (mm) REVERT: U 15 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8407 (pp) REVERT: U 29 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8727 (mptt) REVERT: U 48 LYS cc_start: 0.8449 (pttt) cc_final: 0.8092 (pttp) REVERT: U 63 LYS cc_start: 0.7640 (mttt) cc_final: 0.7369 (mtpp) outliers start: 25 outliers final: 11 residues processed: 270 average time/residue: 0.2946 time to fit residues: 110.7305 Evaluate side-chains 255 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 241 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 THR 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 50 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 8 optimal weight: 0.0770 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 112 GLN D 63 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 73 ASN G 104 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 = 0.3493 r_free = 0.3493 target = 0.060688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.039680 restraints weight = 54078.801| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.48 r_work: 0.2636 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13069 Z= 0.161 Angle : 0.599 7.348 18813 Z= 0.356 Chirality : 0.037 0.175 2149 Planarity : 0.004 0.048 1438 Dihedral : 30.429 149.082 3908 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.68 % Allowed : 14.81 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.30), residues: 828 helix: 1.41 (0.22), residues: 553 sheet: -1.58 (1.10), residues: 19 loop : -1.59 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 164 HIS 0.003 0.001 HIS B 75 PHE 0.012 0.001 PHE D 65 TYR 0.016 0.001 TYR D 83 ARG 0.004 0.000 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.05149 ( 746) hydrogen bonds : angle 2.89359 ( 1855) covalent geometry : bond 0.00350 (13069) covalent geometry : angle 0.59854 (18813) *********************** 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 285 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 266 time to evaluate : 2.518 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: A 50 GLU cc_start: 0.9322 (mt-10) cc_final: 0.8987 (mt-10) REVERT: A 68 GLN cc_start: 0.8985 (tm130) cc_final: 0.8565 (tm-30) REVERT: A 80 THR cc_start: 0.9433 (p) cc_final: 0.9229 (p) REVERT: A 94 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8802 (mm-30) REVERT: A 106 ASP cc_start: 0.8725 (m-30) cc_final: 0.8307 (m-30) REVERT: B 44 LYS cc_start: 0.9156 (mtpt) cc_final: 0.8850 (mtpt) REVERT: B 63 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8489 (mt-10) REVERT: C 57 TYR cc_start: 0.9385 (t80) cc_final: 0.9092 (t80) REVERT: C 64 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8805 (tm-30) REVERT: C 89 ASN cc_start: 0.9484 (m-40) cc_final: 0.9173 (m110) REVERT: D 68 ASP cc_start: 0.9250 (t70) cc_final: 0.8872 (t0) REVERT: E 41 TYR cc_start: 0.8543 (m-80) cc_final: 0.8190 (m-10) REVERT: E 79 LYS cc_start: 0.8915 (tptp) cc_final: 0.8709 (tptm) REVERT: E 93 GLN cc_start: 0.9035 (tp40) cc_final: 0.8723 (tp40) REVERT: E 120 MET cc_start: 0.8878 (mmm) cc_final: 0.8654 (mmm) REVERT: F 25 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8326 (m-40) REVERT: F 62 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9219 (mp) REVERT: G 15 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8247 (tmmt) REVERT: G 56 GLU cc_start: 0.8887 (tt0) cc_final: 0.8475 (mt-10) REVERT: G 89 ASN cc_start: 0.9133 (m110) cc_final: 0.8603 (m110) REVERT: G 92 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8510 (mt-10) REVERT: H 83 TYR cc_start: 0.8535 (m-10) cc_final: 0.8293 (m-80) REVERT: H 93 GLU cc_start: 0.9028 (mp0) cc_final: 0.8659 (mp0) REVERT: S 169 ARG cc_start: 0.8313 (ppt90) cc_final: 0.7978 (ppt170) REVERT: U 13 ILE cc_start: 0.9253 (mm) cc_final: 0.8946 (mm) REVERT: U 15 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8384 (pp) REVERT: U 25 ASN cc_start: 0.9349 (m110) cc_final: 0.9129 (m110) REVERT: U 29 LYS cc_start: 0.9031 (mmmm) cc_final: 0.8737 (mptt) REVERT: U 49 GLN cc_start: 0.8742 (tt0) cc_final: 0.8266 (tt0) REVERT: U 50 LEU cc_start: 0.8622 (mm) cc_final: 0.8162 (mt) outliers start: 19 outliers final: 7 residues processed: 273 average time/residue: 0.3619 time to fit residues: 134.4100 Evaluate side-chains 256 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 246 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 F residue 62 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 103 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN C 112 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 = 0.3493 r_free = 0.3493 target = 0.060670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.039292 restraints weight = 54364.755| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.51 r_work: 0.2627 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13069 Z= 0.163 Angle : 0.590 7.172 18813 Z= 0.350 Chirality : 0.036 0.158 2149 Planarity : 0.004 0.049 1438 Dihedral : 30.309 147.988 3908 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.53 % Allowed : 15.94 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.30), residues: 828 helix: 1.89 (0.22), residues: 552 sheet: -1.61 (1.06), residues: 19 loop : -1.50 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP S 164 HIS 0.003 0.001 HIS B 75 PHE 0.013 0.001 PHE D 65 TYR 0.012 0.001 TYR D 83 ARG 0.003 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.04977 ( 746) hydrogen bonds : angle 2.86977 ( 1855) covalent geometry : bond 0.00357 (13069) covalent geometry : angle 0.59011 (18813) *********************** 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: 25 poor density : 249 time to evaluate : 0.904 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: 0.8962 (mt-10) REVERT: A 94 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8794 (mt-10) REVERT: A 106 ASP cc_start: 0.8571 (m-30) cc_final: 0.8334 (m-30) REVERT: B 63 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8726 (mt-10) REVERT: C 64 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8801 (tm-30) REVERT: D 46 LYS cc_start: 0.9357 (mmmt) cc_final: 0.9142 (mmmt) REVERT: D 68 ASP cc_start: 0.9246 (t70) cc_final: 0.8881 (t0) REVERT: E 41 TYR cc_start: 0.8542 (m-80) cc_final: 0.8196 (m-10) REVERT: E 93 GLN cc_start: 0.9202 (tp40) cc_final: 0.8715 (tp40) REVERT: F 25 ASN cc_start: 0.9159 (OUTLIER) cc_final: 0.8714 (t0) REVERT: G 15 LYS cc_start: 0.8696 (ttmm) cc_final: 0.8260 (tmmt) REVERT: G 56 GLU cc_start: 0.8900 (tt0) cc_final: 0.8462 (mt-10) REVERT: G 89 ASN cc_start: 0.9173 (m110) cc_final: 0.8689 (m110) REVERT: G 92 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8587 (mt-10) REVERT: H 83 TYR cc_start: 0.8530 (m-10) cc_final: 0.8221 (m-10) REVERT: H 93 GLU cc_start: 0.9015 (mp0) cc_final: 0.8658 (mp0) REVERT: H 105 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8178 (tp30) REVERT: U 13 ILE cc_start: 0.9258 (mm) cc_final: 0.8983 (mm) REVERT: U 15 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8609 (pp) REVERT: U 25 ASN cc_start: 0.9335 (m110) cc_final: 0.9125 (m110) REVERT: U 29 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8734 (mptt) REVERT: U 49 GLN cc_start: 0.8623 (tt0) cc_final: 0.7833 (tm-30) REVERT: U 50 LEU cc_start: 0.8031 (mm) cc_final: 0.7759 (mm) REVERT: U 51 GLU cc_start: 0.8625 (mp0) cc_final: 0.7952 (mp0) REVERT: U 64 GLU cc_start: 0.7903 (mp0) cc_final: 0.7614 (mp0) outliers start: 25 outliers final: 10 residues processed: 259 average time/residue: 0.2693 time to fit residues: 95.6509 Evaluate side-chains 252 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 240 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 80 LEU 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 S residue 176 ILE 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 61 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 0.0170 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 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** U 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.061093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.040212 restraints weight = 53148.019| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.46 r_work: 0.2659 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13069 Z= 0.152 Angle : 0.595 8.701 18813 Z= 0.350 Chirality : 0.036 0.155 2149 Planarity : 0.004 0.057 1438 Dihedral : 30.209 147.281 3908 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.39 % Allowed : 18.48 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.31), residues: 828 helix: 2.11 (0.22), residues: 554 sheet: -1.71 (1.09), residues: 19 loop : -1.38 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP S 164 HIS 0.002 0.001 HIS B 75 PHE 0.015 0.001 PHE D 65 TYR 0.022 0.001 TYR C 57 ARG 0.013 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.04905 ( 746) hydrogen bonds : angle 2.80559 ( 1855) covalent geometry : bond 0.00335 (13069) covalent geometry : angle 0.59514 (18813) *********************** 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 270 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9332 (mt-10) cc_final: 0.8973 (mt-10) REVERT: A 94 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8813 (mm-30) REVERT: A 106 ASP cc_start: 0.8566 (m-30) cc_final: 0.8333 (m-30) REVERT: B 23 ARG cc_start: 0.8268 (mmm160) cc_final: 0.7874 (mmm160) REVERT: B 63 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8755 (mt-10) REVERT: C 64 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8912 (tm-30) REVERT: C 89 ASN cc_start: 0.9338 (m-40) cc_final: 0.9038 (m110) REVERT: D 68 ASP cc_start: 0.9239 (t70) cc_final: 0.8823 (t0) REVERT: E 41 TYR cc_start: 0.8514 (m-80) cc_final: 0.8125 (m-10) REVERT: E 93 GLN cc_start: 0.9197 (tp40) cc_final: 0.8693 (tp40) REVERT: F 25 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8699 (t0) REVERT: G 15 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8241 (tmmt) REVERT: G 56 GLU cc_start: 0.8875 (tt0) cc_final: 0.8441 (mt-10) REVERT: G 89 ASN cc_start: 0.9121 (m110) cc_final: 0.8662 (m-40) REVERT: G 92 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8592 (mt-10) REVERT: H 71 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8754 (tp30) REVERT: H 93 GLU cc_start: 0.9010 (mp0) cc_final: 0.8624 (mp0) REVERT: U 11 LYS cc_start: 0.9187 (ttpp) cc_final: 0.8891 (ttpt) REVERT: U 13 ILE cc_start: 0.9272 (mm) cc_final: 0.8560 (mm) REVERT: U 15 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8575 (pp) REVERT: U 25 ASN cc_start: 0.9376 (m110) cc_final: 0.9155 (m110) REVERT: U 29 LYS cc_start: 0.8955 (mmmm) cc_final: 0.8713 (mptt) REVERT: U 49 GLN cc_start: 0.8822 (tt0) cc_final: 0.8039 (tm-30) REVERT: U 51 GLU cc_start: 0.8732 (mp0) cc_final: 0.8130 (mp0) REVERT: U 64 GLU cc_start: 0.7921 (mp0) cc_final: 0.7671 (mp0) outliers start: 24 outliers final: 13 residues processed: 253 average time/residue: 0.3642 time to fit residues: 125.6258 Evaluate side-chains 245 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 230 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 74 GLU 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 G residue 62 ILE Chi-restraints excluded: chain G residue 87 ILE 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 17 VAL Chi-restraints excluded: chain U residue 40 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 75 optimal weight: 20.0000 chunk 44 optimal weight: 0.0040 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.061380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.040598 restraints weight = 53945.614| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.46 r_work: 0.2669 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3507 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= 0.151 Angle : 0.592 7.048 18813 Z= 0.349 Chirality : 0.035 0.154 2149 Planarity : 0.004 0.048 1438 Dihedral : 30.170 146.508 3908 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.31), residues: 828 helix: 2.25 (0.22), residues: 552 sheet: -1.78 (1.11), residues: 19 loop : -1.32 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP S 164 HIS 0.003 0.001 HIS F 75 PHE 0.017 0.001 PHE D 65 TYR 0.021 0.001 TYR C 57 ARG 0.010 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.04880 ( 746) hydrogen bonds : angle 2.78450 ( 1855) covalent geometry : bond 0.00331 (13069) covalent geometry : angle 0.59183 (18813) *********************** 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 263 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8964 (mt-10) REVERT: B 23 ARG cc_start: 0.8375 (mmm160) cc_final: 0.8024 (mmm160) REVERT: B 44 LYS cc_start: 0.9017 (mtpt) cc_final: 0.8696 (mtpp) REVERT: B 63 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8672 (mt-10) REVERT: C 64 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8916 (tm-30) REVERT: C 89 ASN cc_start: 0.9330 (m-40) cc_final: 0.9013 (m110) REVERT: D 68 ASP cc_start: 0.9199 (t70) cc_final: 0.8840 (t0) REVERT: D 108 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8826 (mtmm) REVERT: E 41 TYR cc_start: 0.8502 (m-80) cc_final: 0.8121 (m-10) REVERT: E 79 LYS cc_start: 0.8758 (tptm) cc_final: 0.8523 (tptp) REVERT: E 93 GLN cc_start: 0.9192 (tp40) cc_final: 0.8701 (tp40) REVERT: F 25 ASN cc_start: 0.9103 (OUTLIER) cc_final: 0.8696 (t0) REVERT: F 88 TYR cc_start: 0.9205 (m-10) cc_final: 0.8785 (m-10) REVERT: G 56 GLU cc_start: 0.8879 (tt0) cc_final: 0.8440 (mt-10) REVERT: G 89 ASN cc_start: 0.9099 (m110) cc_final: 0.8665 (m-40) REVERT: G 92 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8571 (mt-10) REVERT: H 71 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8708 (tp30) REVERT: H 83 TYR cc_start: 0.8582 (m-10) cc_final: 0.8162 (m-10) REVERT: H 93 GLU cc_start: 0.8992 (mp0) cc_final: 0.8602 (mp0) REVERT: U 6 LYS cc_start: 0.9092 (ttmt) cc_final: 0.8587 (mmtp) REVERT: U 11 LYS cc_start: 0.9189 (ttpp) cc_final: 0.8893 (ttpt) REVERT: U 13 ILE cc_start: 0.9247 (mm) cc_final: 0.8543 (mm) REVERT: U 15 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8548 (pp) REVERT: U 25 ASN cc_start: 0.9367 (m110) cc_final: 0.9143 (m110) REVERT: U 29 LYS cc_start: 0.8964 (mmmm) cc_final: 0.8727 (mptt) REVERT: U 49 GLN cc_start: 0.8704 (tt0) cc_final: 0.8440 (tp40) outliers start: 21 outliers final: 12 residues processed: 250 average time/residue: 0.2967 time to fit residues: 103.3887 Evaluate side-chains 246 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 41 GLU 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 D residue 108 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 87 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 17 VAL Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 97 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.061014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.039947 restraints weight = 53992.586| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.48 r_work: 0.2652 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13069 Z= 0.168 Angle : 0.615 8.630 18813 Z= 0.358 Chirality : 0.036 0.154 2149 Planarity : 0.004 0.049 1438 Dihedral : 30.203 145.843 3908 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.96 % Allowed : 20.87 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.31), residues: 828 helix: 2.25 (0.22), residues: 552 sheet: -1.74 (1.09), residues: 19 loop : -1.30 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 164 HIS 0.003 0.001 HIS F 75 PHE 0.016 0.001 PHE D 65 TYR 0.022 0.001 TYR C 57 ARG 0.006 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.04926 ( 746) hydrogen bonds : angle 2.82769 ( 1855) covalent geometry : bond 0.00376 (13069) covalent geometry : angle 0.61494 (18813) *********************** 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 257 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8951 (mt-10) REVERT: A 94 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8720 (mt-10) REVERT: A 106 ASP cc_start: 0.8497 (m-30) cc_final: 0.8281 (m-30) REVERT: B 63 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8664 (mt-10) REVERT: B 88 TYR cc_start: 0.9058 (m-80) cc_final: 0.8732 (m-80) REVERT: C 64 GLU cc_start: 0.9174 (tm-30) cc_final: 0.8941 (tm-30) REVERT: C 89 ASN cc_start: 0.9341 (m-40) cc_final: 0.8971 (m110) REVERT: D 46 LYS cc_start: 0.9286 (mmmt) cc_final: 0.8931 (mmmt) REVERT: D 68 ASP cc_start: 0.9235 (t70) cc_final: 0.8872 (t0) REVERT: E 41 TYR cc_start: 0.8519 (m-80) cc_final: 0.8130 (m-10) REVERT: E 79 LYS cc_start: 0.8766 (tptm) cc_final: 0.8544 (tptp) REVERT: E 93 GLN cc_start: 0.9223 (tp40) cc_final: 0.8715 (tp40) REVERT: F 25 ASN cc_start: 0.9083 (OUTLIER) cc_final: 0.8665 (t0) REVERT: F 59 LYS cc_start: 0.9288 (tptt) cc_final: 0.8964 (ttmm) REVERT: G 56 GLU cc_start: 0.8915 (tt0) cc_final: 0.8477 (mt-10) REVERT: G 89 ASN cc_start: 0.9131 (m110) cc_final: 0.8690 (m-40) REVERT: G 92 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8545 (mt-10) REVERT: H 71 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8720 (tp30) REVERT: H 83 TYR cc_start: 0.8591 (m-10) cc_final: 0.8174 (m-10) REVERT: H 93 GLU cc_start: 0.9038 (mp0) cc_final: 0.8635 (mp0) REVERT: U 11 LYS cc_start: 0.9218 (ttpp) cc_final: 0.8919 (ttpt) REVERT: U 13 ILE cc_start: 0.9237 (mm) cc_final: 0.8497 (mm) REVERT: U 15 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8534 (pp) REVERT: U 25 ASN cc_start: 0.9355 (m110) cc_final: 0.9119 (m110) REVERT: U 29 LYS cc_start: 0.8993 (mmmm) cc_final: 0.8760 (mptt) REVERT: U 49 GLN cc_start: 0.8704 (tt0) cc_final: 0.8416 (tp40) outliers start: 21 outliers final: 13 residues processed: 246 average time/residue: 0.3575 time to fit residues: 120.5875 Evaluate side-chains 243 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 228 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU 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 62 LEU Chi-restraints excluded: chain G residue 87 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 17 VAL Chi-restraints excluded: chain U residue 40 GLN Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 105 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS 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 = 0.3445 r_free = 0.3445 target = 0.058943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.037562 restraints weight = 54744.145| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.45 r_work: 0.2551 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 13069 Z= 0.300 Angle : 0.700 7.879 18813 Z= 0.399 Chirality : 0.041 0.188 2149 Planarity : 0.005 0.074 1438 Dihedral : 30.588 146.259 3908 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.10 % Allowed : 20.17 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.30), residues: 828 helix: 1.93 (0.22), residues: 551 sheet: -1.94 (1.00), residues: 19 loop : -1.35 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP S 164 HIS 0.006 0.001 HIS A 113 PHE 0.013 0.002 PHE D 65 TYR 0.027 0.002 TYR C 57 ARG 0.018 0.001 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.05923 ( 746) hydrogen bonds : angle 3.19568 ( 1855) covalent geometry : bond 0.00678 (13069) covalent geometry : angle 0.69956 (18813) *********************** 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 245 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9332 (mt-10) cc_final: 0.8991 (mt-10) REVERT: A 94 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8772 (mt-10) REVERT: B 63 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8786 (mt-10) REVERT: C 64 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8907 (tm-30) REVERT: C 89 ASN cc_start: 0.9399 (m-40) cc_final: 0.9080 (m110) REVERT: C 118 LYS cc_start: 0.7401 (tppt) cc_final: 0.7107 (tppt) REVERT: E 41 TYR cc_start: 0.8620 (m-80) cc_final: 0.8281 (m-10) REVERT: E 79 LYS cc_start: 0.8839 (tptm) cc_final: 0.8586 (tptp) REVERT: E 93 GLN cc_start: 0.9311 (tp40) cc_final: 0.8669 (tp40) REVERT: F 25 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8160 (m-40) REVERT: F 88 TYR cc_start: 0.9298 (m-10) cc_final: 0.8719 (m-10) REVERT: H 71 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8761 (tp30) REVERT: H 83 TYR cc_start: 0.8577 (m-10) cc_final: 0.8299 (m-10) REVERT: H 93 GLU cc_start: 0.9079 (mp0) cc_final: 0.8596 (mp0) REVERT: U 6 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8601 (mmtp) REVERT: U 11 LYS cc_start: 0.9293 (ttpp) cc_final: 0.9017 (ttpt) REVERT: U 13 ILE cc_start: 0.9248 (mm) cc_final: 0.8478 (mm) REVERT: U 25 ASN cc_start: 0.9362 (m110) cc_final: 0.9109 (m110) REVERT: U 29 LYS cc_start: 0.8982 (mmmm) cc_final: 0.8670 (mptt) outliers start: 22 outliers final: 16 residues processed: 234 average time/residue: 0.3441 time to fit residues: 109.4616 Evaluate side-chains 234 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU 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 E residue 74 ILE Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 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 17 VAL Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 44 ILE 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 76 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** 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 68 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.059374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.038324 restraints weight = 54517.759| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.43 r_work: 0.2582 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 13069 Z= 0.230 Angle : 0.666 7.059 18813 Z= 0.383 Chirality : 0.038 0.177 2149 Planarity : 0.005 0.066 1438 Dihedral : 30.463 145.923 3908 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.96 % Allowed : 21.30 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.30), residues: 828 helix: 1.95 (0.22), residues: 551 sheet: -1.84 (1.02), residues: 19 loop : -1.33 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP S 164 HIS 0.005 0.001 HIS A 113 PHE 0.016 0.002 PHE D 65 TYR 0.023 0.002 TYR C 57 ARG 0.016 0.001 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.05274 ( 746) hydrogen bonds : angle 3.06793 ( 1855) covalent geometry : bond 0.00520 (13069) covalent geometry : angle 0.66568 (18813) *********************** 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: 21 poor density : 227 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9324 (mt-10) cc_final: 0.8972 (mt-10) REVERT: A 79 LYS cc_start: 0.8817 (tptp) cc_final: 0.8564 (tptp) REVERT: A 97 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8511 (mm-30) REVERT: B 63 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8756 (mt-10) REVERT: B 79 LYS cc_start: 0.9496 (mmtp) cc_final: 0.8860 (mtmt) REVERT: C 64 GLU cc_start: 0.9229 (tm-30) cc_final: 0.9015 (tm-30) REVERT: C 89 ASN cc_start: 0.9419 (m-40) cc_final: 0.9120 (m110) REVERT: D 68 ASP cc_start: 0.9271 (t70) cc_final: 0.8850 (t0) REVERT: E 41 TYR cc_start: 0.8631 (m-80) cc_final: 0.8257 (m-10) REVERT: E 79 LYS cc_start: 0.8820 (tptm) cc_final: 0.8567 (tptp) REVERT: E 93 GLN cc_start: 0.9268 (tp40) cc_final: 0.8661 (tp40) REVERT: F 25 ASN cc_start: 0.9043 (OUTLIER) cc_final: 0.8516 (m-40) REVERT: G 92 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8529 (mt-10) REVERT: H 71 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8760 (tp30) REVERT: H 83 TYR cc_start: 0.8527 (m-10) cc_final: 0.8293 (m-10) REVERT: H 93 GLU cc_start: 0.9091 (mp0) cc_final: 0.8660 (mp0) REVERT: H 105 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8252 (tp30) REVERT: U 13 ILE cc_start: 0.9264 (mm) cc_final: 0.9018 (mm) REVERT: U 25 ASN cc_start: 0.9347 (m110) cc_final: 0.9129 (m110) REVERT: U 29 LYS cc_start: 0.8927 (mmmm) cc_final: 0.8646 (mptt) REVERT: U 64 GLU cc_start: 0.7982 (mp0) cc_final: 0.7739 (mp0) REVERT: U 68 HIS cc_start: 0.8411 (m-70) cc_final: 0.8084 (m90) outliers start: 21 outliers final: 14 residues processed: 239 average time/residue: 0.3022 time to fit residues: 100.5140 Evaluate side-chains 236 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 221 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU 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 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 30 ILE Chi-restraints excluded: chain U residue 60 ASN 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 25 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 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 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 = 0.3499 r_free = 0.3499 target = 0.060917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.039680 restraints weight = 53879.069| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.49 r_work: 0.2640 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13069 Z= 0.159 Angle : 0.631 7.471 18813 Z= 0.365 Chirality : 0.036 0.163 2149 Planarity : 0.004 0.062 1438 Dihedral : 30.162 145.627 3908 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.26 % Allowed : 21.44 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.31), residues: 828 helix: 2.10 (0.22), residues: 555 sheet: -1.85 (1.03), residues: 19 loop : -1.19 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 164 HIS 0.002 0.001 HIS F 75 PHE 0.019 0.001 PHE D 65 TYR 0.023 0.001 TYR C 57 ARG 0.014 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.05000 ( 746) hydrogen bonds : angle 2.90436 ( 1855) covalent geometry : bond 0.00352 (13069) covalent geometry : angle 0.63062 (18813) ********************** 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 249 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9326 (mt-10) cc_final: 0.8959 (mt-10) REVERT: A 79 LYS cc_start: 0.8834 (tptp) cc_final: 0.8581 (tptp) REVERT: A 97 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8631 (mm-30) REVERT: B 22 LEU cc_start: 0.8707 (mt) cc_final: 0.8298 (mt) REVERT: B 63 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8732 (mt-10) REVERT: B 79 LYS cc_start: 0.9473 (mmtp) cc_final: 0.8818 (mtmt) REVERT: B 88 TYR cc_start: 0.9030 (m-80) cc_final: 0.8710 (m-80) REVERT: C 64 GLU cc_start: 0.9178 (tm-30) cc_final: 0.8943 (tm-30) REVERT: C 89 ASN cc_start: 0.9401 (m-40) cc_final: 0.8990 (m110) REVERT: D 68 ASP cc_start: 0.9230 (t70) cc_final: 0.8831 (t0) REVERT: E 41 TYR cc_start: 0.8605 (m-80) cc_final: 0.8214 (m-10) REVERT: E 79 LYS cc_start: 0.8824 (tptm) cc_final: 0.8570 (tptp) REVERT: E 93 GLN cc_start: 0.9207 (tp40) cc_final: 0.8679 (tp40) REVERT: E 99 TYR cc_start: 0.9227 (t80) cc_final: 0.8862 (t80) REVERT: F 25 ASN cc_start: 0.9065 (OUTLIER) cc_final: 0.8719 (m-40) REVERT: G 92 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8523 (mt-10) REVERT: H 93 GLU cc_start: 0.9087 (mp0) cc_final: 0.8667 (mp0) REVERT: H 105 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8219 (tp30) REVERT: U 13 ILE cc_start: 0.9224 (mm) cc_final: 0.8985 (mm) REVERT: U 29 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8708 (mptt) REVERT: U 64 GLU cc_start: 0.7978 (mp0) cc_final: 0.7674 (mp0) outliers start: 16 outliers final: 13 residues processed: 243 average time/residue: 0.2647 time to fit residues: 89.0873 Evaluate side-chains 237 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 41 GLU 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 62 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 30 ILE Chi-restraints excluded: chain U residue 50 LEU 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 74 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 99 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 U 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.060659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.039196 restraints weight = 53917.126| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.46 r_work: 0.2620 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13069 Z= 0.183 Angle : 0.651 10.067 18813 Z= 0.374 Chirality : 0.036 0.166 2149 Planarity : 0.004 0.048 1438 Dihedral : 30.242 145.970 3908 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.12 % Allowed : 22.71 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.31), residues: 828 helix: 2.06 (0.22), residues: 555 sheet: -1.86 (1.02), residues: 19 loop : -1.15 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 164 HIS 0.004 0.001 HIS B 75 PHE 0.017 0.001 PHE D 65 TYR 0.062 0.002 TYR H 83 ARG 0.007 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.05013 ( 746) hydrogen bonds : angle 2.97122 ( 1855) covalent geometry : bond 0.00413 (13069) covalent geometry : angle 0.65115 (18813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7997.81 seconds wall clock time: 143 minutes 20.98 seconds (8600.98 seconds total)