Starting phenix.real_space_refine on Wed Mar 12 07:55:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g0b_29652/03_2025/8g0b_29652.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g0b_29652/03_2025/8g0b_29652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g0b_29652/03_2025/8g0b_29652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g0b_29652/03_2025/8g0b_29652.map" model { file = "/net/cci-nas-00/data/ceres_data/8g0b_29652/03_2025/8g0b_29652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g0b_29652/03_2025/8g0b_29652.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.199 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Br 7 7.06 5 S 26 5.16 5 C 5189 2.51 5 N 1236 2.21 5 O 1300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7758 Number of models: 1 Model: "" Number of chains: 19 Chain: "1" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "3" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "4" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 554 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "5" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 564 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "6" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "7" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "8" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "9" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "a" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1807 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "b" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 322 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "d" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 37} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "1" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YGR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.51, per 1000 atoms: 0.71 Number of scatterers: 7758 At special positions: 0 Unit cell: (79.31, 97.85, 83.43, 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) Br 7 34.99 S 26 16.00 O 1300 8.00 N 1236 7.00 C 5189 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: 2.23 Conformation dependent library (CDL) restraints added in 1.1 seconds 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 2 sheets defined 88.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain '1' and resid 5 through 46 Processing helix chain '1' and resid 49 through 80 removed outlier: 4.528A pdb=" N THR 1 55 " --> pdb=" O GLY 1 51 " (cutoff:3.500A) Proline residue: 1 56 - end of helix Processing helix chain '2' and resid 6 through 46 Processing helix chain '2' and resid 49 through 80 removed outlier: 4.042A pdb=" N THR 2 55 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) Proline residue: 2 56 - end of helix Processing helix chain '3' and resid 6 through 46 Processing helix chain '3' and resid 49 through 80 removed outlier: 4.646A pdb=" N THR 3 55 " --> pdb=" O GLY 3 51 " (cutoff:3.500A) Proline residue: 3 56 - end of helix removed outlier: 3.684A pdb=" N ASN 3 71 " --> pdb=" O ALA 3 67 " (cutoff:3.500A) Processing helix chain '4' and resid 6 through 46 Processing helix chain '4' and resid 49 through 81 removed outlier: 3.882A pdb=" N THR 4 55 " --> pdb=" O GLY 4 51 " (cutoff:3.500A) Proline residue: 4 56 - end of helix Processing helix chain '5' and resid 6 through 46 Processing helix chain '5' and resid 49 through 81 removed outlier: 4.481A pdb=" N THR 5 55 " --> pdb=" O GLY 5 51 " (cutoff:3.500A) Proline residue: 5 56 - end of helix removed outlier: 3.553A pdb=" N ALA 5 67 " --> pdb=" O LEU 5 63 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR 5 68 " --> pdb=" O VAL 5 64 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA 5 76 " --> pdb=" O LEU 5 72 " (cutoff:3.500A) Processing helix chain '6' and resid 6 through 46 Processing helix chain '6' and resid 49 through 81 removed outlier: 3.847A pdb=" N THR 6 55 " --> pdb=" O GLY 6 51 " (cutoff:3.500A) Proline residue: 6 56 - end of helix removed outlier: 3.524A pdb=" N TYR 6 68 " --> pdb=" O VAL 6 64 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA 6 76 " --> pdb=" O LEU 6 72 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU 6 77 " --> pdb=" O ALA 6 73 " (cutoff:3.500A) Processing helix chain '7' and resid 6 through 46 Processing helix chain '7' and resid 47 through 50 Processing helix chain '7' and resid 53 through 80 Processing helix chain '8' and resid 6 through 46 Processing helix chain '8' and resid 49 through 80 removed outlier: 3.791A pdb=" N THR 8 55 " --> pdb=" O GLY 8 51 " (cutoff:3.500A) Proline residue: 8 56 - end of helix removed outlier: 3.529A pdb=" N ALA 8 67 " --> pdb=" O LEU 8 63 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA 8 76 " --> pdb=" O LEU 8 72 " (cutoff:3.500A) Processing helix chain '9' and resid 6 through 46 Processing helix chain '9' and resid 48 through 81 removed outlier: 4.550A pdb=" N ARG 9 52 " --> pdb=" O GLU 9 48 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE 9 54 " --> pdb=" O GLN 9 50 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR 9 55 " --> pdb=" O GLY 9 51 " (cutoff:3.500A) Proline residue: 9 56 - end of helix removed outlier: 3.785A pdb=" N ALA 9 67 " --> pdb=" O LEU 9 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 52 Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 106 removed outlier: 3.775A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 109 No H-bonds generated for 'chain 'a' and resid 107 through 109' Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 154 removed outlier: 3.626A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 165 removed outlier: 3.633A pdb=" N ILE a 160 " --> pdb=" O VAL a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 167 through 169 No H-bonds generated for 'chain 'a' and resid 167 through 169' Processing helix chain 'a' and resid 170 through 205 Proline residue: a 182 - end of helix removed outlier: 3.906A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN a 192 " --> pdb=" O ARG a 188 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 246 removed outlier: 3.922A pdb=" N TRP a 212 " --> pdb=" O TRP a 208 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 4.001A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 48 removed outlier: 3.744A pdb=" N ILE b 37 " --> pdb=" O ALA b 33 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 64 Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 24 through 40 removed outlier: 4.093A pdb=" N MET d 30 " --> pdb=" O VAL d 26 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'a' and resid 112 through 114 741 hydrogen bonds defined for protein. 2211 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 2362 1.34 - 1.49: 2225 1.49 - 1.64: 3299 1.64 - 1.78: 2 1.78 - 1.93: 56 Bond restraints: 7944 Sorted by residual: bond pdb=" CA ARG d 27 " pdb=" C ARG d 27 " ideal model delta sigma weight residual 1.519 1.448 0.071 1.22e-02 6.72e+03 3.37e+01 bond pdb=" CA VAL d 26 " pdb=" C VAL d 26 " ideal model delta sigma weight residual 1.523 1.449 0.074 1.27e-02 6.20e+03 3.37e+01 bond pdb=" C31 YGR 9 601 " pdb=" O32 YGR 9 601 " ideal model delta sigma weight residual 1.335 1.432 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C31 YGR 6 601 " pdb=" O32 YGR 6 601 " ideal model delta sigma weight residual 1.335 1.429 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" N VAL d 26 " pdb=" CA VAL d 26 " ideal model delta sigma weight residual 1.459 1.401 0.058 1.25e-02 6.40e+03 2.18e+01 ... (remaining 7939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 10542 1.94 - 3.89: 209 3.89 - 5.83: 65 5.83 - 7.78: 5 7.78 - 9.72: 1 Bond angle restraints: 10822 Sorted by residual: angle pdb=" N ARG d 27 " pdb=" CA ARG d 27 " pdb=" C ARG d 27 " ideal model delta sigma weight residual 113.55 103.83 9.72 1.26e+00 6.30e-01 5.95e+01 angle pdb=" N THR d 28 " pdb=" CA THR d 28 " pdb=" C THR d 28 " ideal model delta sigma weight residual 110.97 103.89 7.08 1.09e+00 8.42e-01 4.21e+01 angle pdb=" C VAL d 26 " pdb=" CA VAL d 26 " pdb=" CB VAL d 26 " ideal model delta sigma weight residual 111.29 103.66 7.63 1.64e+00 3.72e-01 2.16e+01 angle pdb=" N ILE a 210 " pdb=" CA ILE a 210 " pdb=" C ILE a 210 " ideal model delta sigma weight residual 113.20 109.72 3.48 9.60e-01 1.09e+00 1.32e+01 angle pdb=" C THR d 28 " pdb=" N LEU d 29 " pdb=" CA LEU d 29 " ideal model delta sigma weight residual 120.82 116.64 4.18 1.50e+00 4.44e-01 7.76e+00 ... (remaining 10817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.07: 4455 35.07 - 70.14: 66 70.14 - 105.22: 19 105.22 - 140.29: 0 140.29 - 175.36: 1 Dihedral angle restraints: 4541 sinusoidal: 1739 harmonic: 2802 Sorted by residual: dihedral pdb=" C26 YGR 8 601 " pdb=" C27 YGR 8 601 " pdb=" O28 YGR 8 601 " pdb=" C29 YGR 8 601 " ideal model delta sinusoidal sigma weight residual 178.39 -6.25 -175.36 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C VAL d 26 " pdb=" N VAL d 26 " pdb=" CA VAL d 26 " pdb=" CB VAL d 26 " ideal model delta harmonic sigma weight residual -122.00 -113.36 -8.64 0 2.50e+00 1.60e-01 1.20e+01 dihedral pdb=" C26 YGR 6 601 " pdb=" C27 YGR 6 601 " pdb=" O28 YGR 6 601 " pdb=" C29 YGR 6 601 " ideal model delta sinusoidal sigma weight residual 178.39 -87.62 -93.99 1 3.00e+01 1.11e-03 1.14e+01 ... (remaining 4538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1021 0.057 - 0.114: 215 0.114 - 0.171: 5 0.171 - 0.227: 1 0.227 - 0.284: 6 Chirality restraints: 1248 Sorted by residual: chirality pdb=" C05 YGR 7 601 " pdb=" C04 YGR 7 601 " pdb=" C06 YGR 7 601 " pdb=" C18 YGR 7 601 " both_signs ideal model delta sigma weight residual False -2.41 -2.69 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C05 YGR 6 601 " pdb=" C04 YGR 6 601 " pdb=" C06 YGR 6 601 " pdb=" C18 YGR 6 601 " both_signs ideal model delta sigma weight residual False -2.41 -2.69 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C05 YGR 5 601 " pdb=" C04 YGR 5 601 " pdb=" C06 YGR 5 601 " pdb=" C18 YGR 5 601 " both_signs ideal model delta sigma weight residual False -2.41 -2.68 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1245 not shown) Planarity restraints: 1329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN 1 46 " -0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO 1 47 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO 1 47 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO 1 47 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN 5 46 " 0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO 5 47 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO 5 47 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO 5 47 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C05 YGR 8 601 " -0.018 2.00e-02 2.50e+03 8.56e-03 1.83e+00 pdb=" C06 YGR 8 601 " 0.012 2.00e-02 2.50e+03 pdb=" C07 YGR 8 601 " -0.001 2.00e-02 2.50e+03 pdb=" C10 YGR 8 601 " 0.003 2.00e-02 2.50e+03 pdb=" C14 YGR 8 601 " 0.004 2.00e-02 2.50e+03 pdb=" C17 YGR 8 601 " 0.009 2.00e-02 2.50e+03 pdb=" N13 YGR 8 601 " -0.006 2.00e-02 2.50e+03 pdb=" O08 YGR 8 601 " 0.009 2.00e-02 2.50e+03 pdb=" O11 YGR 8 601 " -0.007 2.00e-02 2.50e+03 pdb=" O15 YGR 8 601 " -0.004 2.00e-02 2.50e+03 ... (remaining 1326 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1481 2.76 - 3.29: 8361 3.29 - 3.83: 14338 3.83 - 4.36: 16914 4.36 - 4.90: 29235 Nonbonded interactions: 70329 Sorted by model distance: nonbonded pdb=" OE1 GLU 7 65 " pdb=" N21 YGR 7 601 " model vdw 2.221 3.120 nonbonded pdb=" OD1 ASN a 132 " pdb=" N ASN b 28 " model vdw 2.280 3.120 nonbonded pdb=" OE1 GLU 8 65 " pdb=" N21 YGR 8 601 " model vdw 2.301 3.120 nonbonded pdb=" N ASN a 28 " pdb=" OG1 THR b 30 " model vdw 2.305 3.120 nonbonded pdb=" OE1 GLU 5 65 " pdb=" N21 YGR 5 601 " model vdw 2.345 3.120 ... (remaining 70324 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 '1' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '2' and (resid 5 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 85)) selection = (chain '3' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '4' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 85)) selection = (chain '5' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 or (resid 48 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 51 or (resid 52 and (n \ ame N or name CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '6' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '7' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 51 or (resid 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 85)) selection = (chain '8' and (resid 5 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 85)) selection = (chain '9' and (resid 5 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 85)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.550 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 : 0.008 0.097 7944 Z= 0.526 Angle : 0.697 9.721 10822 Z= 0.336 Chirality : 0.044 0.284 1248 Planarity : 0.005 0.050 1329 Dihedral : 15.192 175.362 2785 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.14 % Allowed : 0.29 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1018 helix: 0.84 (0.18), residues: 874 sheet: -3.10 (1.56), residues: 9 loop : -1.08 (0.63), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.002 0.001 HIS a 158 PHE 0.016 0.001 PHE a 142 TYR 0.009 0.001 TYR a 145 ARG 0.006 0.001 ARG b 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: d 27 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6810 (tpp-160) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.9732 time to fit residues: 145.0219 Evaluate side-chains 116 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 0.0050 chunk 41 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.0570 chunk 93 optimal weight: 2.9990 overall best weight: 0.4312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 46 GLN 6 46 GLN ** d 7 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 = 0.3619 r_free = 0.3619 target = 0.137914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117229 restraints weight = 6641.396| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.02 r_work: 0.3273 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7944 Z= 0.223 Angle : 0.584 6.888 10822 Z= 0.305 Chirality : 0.041 0.149 1248 Planarity : 0.005 0.048 1329 Dihedral : 11.174 161.173 1341 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.43 % Allowed : 8.88 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.27), residues: 1018 helix: 2.24 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -0.23 (0.66), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.003 0.001 HIS a 12 PHE 0.021 0.002 PHE a 142 TYR 0.010 0.001 TYR a 145 ARG 0.006 0.001 ARG a 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: 1 63 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8186 (mm) REVERT: 7 69 PHE cc_start: 0.8610 (t80) cc_final: 0.8275 (t80) REVERT: a 205 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8216 (mtp) REVERT: d 27 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6462 (tpp-160) outliers start: 10 outliers final: 2 residues processed: 129 average time/residue: 1.0234 time to fit residues: 141.3985 Evaluate side-chains 111 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 3 residue 21 MET Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 68 optimal weight: 0.0570 chunk 41 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 46 GLN 9 50 GLN ** d 7 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 = 0.3648 r_free = 0.3648 target = 0.139874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.118433 restraints weight = 6474.599| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.02 r_work: 0.3266 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7944 Z= 0.213 Angle : 0.561 7.945 10822 Z= 0.289 Chirality : 0.041 0.142 1248 Planarity : 0.004 0.046 1329 Dihedral : 9.433 151.724 1341 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.15 % Allowed : 10.32 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.27), residues: 1018 helix: 2.51 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -0.19 (0.66), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 208 HIS 0.003 0.001 HIS a 146 PHE 0.020 0.001 PHE a 142 TYR 0.034 0.002 TYR a 145 ARG 0.007 0.001 ARG a 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: 1 63 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8169 (mm) REVERT: 3 8 ILE cc_start: 0.9031 (mp) cc_final: 0.8723 (tt) REVERT: 6 75 MET cc_start: 0.8391 (tmm) cc_final: 0.7975 (tmm) REVERT: 7 69 PHE cc_start: 0.8608 (t80) cc_final: 0.8263 (t80) REVERT: d 27 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6584 (tpp-160) outliers start: 15 outliers final: 2 residues processed: 134 average time/residue: 0.9945 time to fit residues: 142.8005 Evaluate side-chains 116 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 3 residue 21 MET Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 72 optimal weight: 0.0000 chunk 20 optimal weight: 0.0670 chunk 11 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 6 ASN ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 46 GLN 9 50 GLN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117348 restraints weight = 6524.029| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.01 r_work: 0.3278 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7944 Z= 0.211 Angle : 0.558 8.263 10822 Z= 0.286 Chirality : 0.041 0.144 1248 Planarity : 0.004 0.045 1329 Dihedral : 8.377 145.227 1341 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.58 % Allowed : 12.61 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.27), residues: 1018 helix: 2.54 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -0.39 (0.63), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 208 HIS 0.003 0.001 HIS a 146 PHE 0.019 0.001 PHE a 142 TYR 0.037 0.002 TYR a 145 ARG 0.008 0.001 ARG a 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: 3 8 ILE cc_start: 0.9025 (mp) cc_final: 0.8742 (tt) REVERT: 6 75 MET cc_start: 0.8410 (tmm) cc_final: 0.7999 (tmm) REVERT: 7 69 PHE cc_start: 0.8568 (t80) cc_final: 0.8248 (t80) REVERT: d 27 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6571 (tpp-160) outliers start: 11 outliers final: 3 residues processed: 130 average time/residue: 0.9793 time to fit residues: 136.2187 Evaluate side-chains 121 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 3 residue 21 MET Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 20 optimal weight: 0.0470 chunk 76 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 46 GLN 9 50 GLN ** d 7 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 = 0.3663 r_free = 0.3663 target = 0.141176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119497 restraints weight = 6472.942| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.03 r_work: 0.3281 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7944 Z= 0.201 Angle : 0.554 8.440 10822 Z= 0.282 Chirality : 0.040 0.144 1248 Planarity : 0.004 0.045 1329 Dihedral : 7.781 139.327 1341 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.72 % Allowed : 13.47 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.40 (0.26), residues: 1018 helix: 2.59 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -0.49 (0.61), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.019 0.001 PHE a 142 TYR 0.039 0.002 TYR a 145 ARG 0.007 0.001 ARG a 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.767 Fit side-chains REVERT: 3 8 ILE cc_start: 0.8918 (mp) cc_final: 0.8654 (tt) REVERT: 6 75 MET cc_start: 0.8436 (tmm) cc_final: 0.7912 (tmm) REVERT: 7 69 PHE cc_start: 0.8534 (t80) cc_final: 0.8197 (t80) REVERT: d 27 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6544 (tpp-160) outliers start: 12 outliers final: 5 residues processed: 131 average time/residue: 0.9938 time to fit residues: 139.4079 Evaluate side-chains 120 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 3 residue 21 MET Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 23 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 46 GLN 9 50 GLN a 112 GLN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.138804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.117224 restraints weight = 6474.879| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.02 r_work: 0.3259 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7944 Z= 0.243 Angle : 0.583 9.333 10822 Z= 0.296 Chirality : 0.041 0.146 1248 Planarity : 0.004 0.047 1329 Dihedral : 7.441 135.847 1341 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.01 % Allowed : 13.32 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.26), residues: 1018 helix: 2.53 (0.17), residues: 894 sheet: -2.87 (1.59), residues: 9 loop : -0.36 (0.63), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.023 0.002 PHE 3 74 TYR 0.039 0.002 TYR a 145 ARG 0.007 0.001 ARG a 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.765 Fit side-chains REVERT: 3 8 ILE cc_start: 0.8908 (mp) cc_final: 0.8661 (tt) REVERT: 6 75 MET cc_start: 0.8451 (tmm) cc_final: 0.7920 (tmm) REVERT: 7 69 PHE cc_start: 0.8583 (t80) cc_final: 0.8244 (t80) REVERT: a 222 ASP cc_start: 0.8139 (t0) cc_final: 0.7802 (t0) REVERT: a 243 GLN cc_start: 0.8466 (mt0) cc_final: 0.8229 (mt0) REVERT: d 27 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6544 (tpp-160) outliers start: 14 outliers final: 6 residues processed: 128 average time/residue: 1.0086 time to fit residues: 138.2822 Evaluate side-chains 122 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 3 residue 21 MET Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 13 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 46 GLN 9 50 GLN 9 71 ASN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117309 restraints weight = 6527.089| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.02 r_work: 0.3254 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7944 Z= 0.238 Angle : 0.588 10.205 10822 Z= 0.298 Chirality : 0.041 0.143 1248 Planarity : 0.004 0.044 1329 Dihedral : 7.124 130.505 1341 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.72 % Allowed : 14.76 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.26), residues: 1018 helix: 2.52 (0.17), residues: 894 sheet: -2.83 (1.60), residues: 9 loop : -0.38 (0.63), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.020 0.001 PHE 3 74 TYR 0.039 0.002 TYR a 145 ARG 0.007 0.001 ARG a 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.803 Fit side-chains REVERT: 1 63 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8135 (mm) REVERT: 3 8 ILE cc_start: 0.8903 (mp) cc_final: 0.8671 (tt) REVERT: 6 75 MET cc_start: 0.8445 (tmm) cc_final: 0.7962 (tmm) REVERT: 7 69 PHE cc_start: 0.8583 (t80) cc_final: 0.8247 (t80) REVERT: d 27 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6659 (tpp-160) outliers start: 12 outliers final: 5 residues processed: 123 average time/residue: 1.0175 time to fit residues: 133.9714 Evaluate side-chains 119 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 3 residue 21 MET Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 46 GLN 9 50 GLN a 243 GLN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117207 restraints weight = 6575.934| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.03 r_work: 0.3257 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7944 Z= 0.236 Angle : 0.592 10.847 10822 Z= 0.300 Chirality : 0.041 0.162 1248 Planarity : 0.004 0.045 1329 Dihedral : 6.953 124.979 1341 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.01 % Allowed : 14.61 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.26), residues: 1018 helix: 2.51 (0.17), residues: 894 sheet: -2.84 (1.59), residues: 9 loop : -0.42 (0.62), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.019 0.002 PHE 6 74 TYR 0.040 0.002 TYR a 145 ARG 0.008 0.001 ARG a 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.793 Fit side-chains REVERT: 1 63 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8140 (mm) REVERT: 3 8 ILE cc_start: 0.8899 (mp) cc_final: 0.8685 (tt) REVERT: 6 75 MET cc_start: 0.8450 (tmm) cc_final: 0.7894 (tmm) REVERT: 7 69 PHE cc_start: 0.8566 (t80) cc_final: 0.8227 (t80) REVERT: a 222 ASP cc_start: 0.8132 (t0) cc_final: 0.7796 (t0) REVERT: b 63 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7244 (ttp) REVERT: d 27 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6768 (tpp-160) outliers start: 14 outliers final: 5 residues processed: 122 average time/residue: 1.0487 time to fit residues: 136.9851 Evaluate side-chains 119 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 3 residue 21 MET Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 7 residue 8 ILE Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 45 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 46 GLN 6 71 ASN 9 50 GLN a 243 GLN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117913 restraints weight = 6592.234| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.03 r_work: 0.3261 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7944 Z= 0.227 Angle : 0.605 11.281 10822 Z= 0.306 Chirality : 0.042 0.173 1248 Planarity : 0.005 0.076 1329 Dihedral : 6.842 117.848 1341 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.86 % Allowed : 15.62 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.26), residues: 1018 helix: 2.50 (0.17), residues: 895 sheet: -2.83 (1.60), residues: 9 loop : -0.41 (0.62), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.018 0.001 PHE 3 74 TYR 0.041 0.002 TYR a 145 ARG 0.009 0.001 ARG 3 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.774 Fit side-chains REVERT: 1 63 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8118 (mm) REVERT: 6 75 MET cc_start: 0.8470 (tmm) cc_final: 0.7902 (tmm) REVERT: 7 69 PHE cc_start: 0.8557 (t80) cc_final: 0.8223 (t80) REVERT: a 222 ASP cc_start: 0.8132 (t0) cc_final: 0.7795 (t0) REVERT: b 63 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7215 (ttp) REVERT: d 27 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6804 (tpp-160) outliers start: 13 outliers final: 4 residues processed: 117 average time/residue: 1.0661 time to fit residues: 133.3986 Evaluate side-chains 113 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain a residue 111 LEU Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain d residue 27 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 83 optimal weight: 0.0870 chunk 56 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 63 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 76 optimal weight: 0.0770 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 50 GLN a 243 GLN ** d 7 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 = 0.3703 r_free = 0.3703 target = 0.144647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.123374 restraints weight = 6607.893| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.02 r_work: 0.3337 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7944 Z= 0.178 Angle : 0.582 11.863 10822 Z= 0.289 Chirality : 0.041 0.147 1248 Planarity : 0.004 0.056 1329 Dihedral : 6.633 102.512 1341 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.86 % Allowed : 17.05 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.26), residues: 1018 helix: 2.63 (0.17), residues: 895 sheet: -2.83 (1.57), residues: 9 loop : -0.43 (0.62), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.004 0.001 HIS a 146 PHE 0.019 0.001 PHE a 142 TYR 0.038 0.002 TYR a 145 ARG 0.008 0.001 ARG a 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.765 Fit side-chains REVERT: 6 75 MET cc_start: 0.8407 (tmm) cc_final: 0.7843 (tmm) REVERT: 7 69 PHE cc_start: 0.8493 (t80) cc_final: 0.8203 (t80) REVERT: a 222 ASP cc_start: 0.8151 (t0) cc_final: 0.7820 (t0) REVERT: d 27 ARG cc_start: 0.7609 (ttt90) cc_final: 0.6867 (tpp-160) outliers start: 6 outliers final: 3 residues processed: 119 average time/residue: 0.9358 time to fit residues: 119.7713 Evaluate side-chains 110 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain a residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 10 optimal weight: 4.9990 chunk 47 optimal weight: 0.0270 chunk 88 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 6 ASN 5 46 GLN 9 50 GLN a 243 GLN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121323 restraints weight = 6582.756| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.03 r_work: 0.3303 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7944 Z= 0.212 Angle : 0.617 12.645 10822 Z= 0.307 Chirality : 0.041 0.205 1248 Planarity : 0.005 0.055 1329 Dihedral : 6.483 91.267 1337 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.00 % Allowed : 17.19 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.26), residues: 1018 helix: 2.60 (0.17), residues: 895 sheet: -2.72 (1.60), residues: 9 loop : -0.43 (0.61), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 218 HIS 0.004 0.001 HIS a 146 PHE 0.017 0.001 PHE a 142 TYR 0.008 0.001 TYR 4 68 ARG 0.008 0.001 ARG a 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5057.78 seconds wall clock time: 86 minutes 57.87 seconds (5217.87 seconds total)