Starting phenix.real_space_refine on Sat Dec 28 03:15:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g0b_29652/12_2024/8g0b_29652.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g0b_29652/12_2024/8g0b_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_29652/12_2024/8g0b_29652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g0b_29652/12_2024/8g0b_29652.map" model { file = "/net/cci-nas-00/data/ceres_data/8g0b_29652/12_2024/8g0b_29652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g0b_29652/12_2024/8g0b_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.68, per 1000 atoms: 0.73 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: 2.42 Conformation dependent library (CDL) restraints added in 1.2 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: 0.67 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: 2.29 Time building geometry restraints manager: 2.65 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: 1.520 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.470 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.010 ------------------------------------------------------------------------------- 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 : 0.809 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: 1.0048 time to fit residues: 149.8240 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 : 0.795 ------------------------------------------------------------------------------- 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: 0.4980 chunk 93 optimal weight: 2.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7944 Z= 0.232 Angle : 0.586 6.902 10822 Z= 0.306 Chirality : 0.042 0.149 1248 Planarity : 0.005 0.048 1329 Dihedral : 11.047 160.305 1341 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.43 % Allowed : 9.03 % Favored : 89.54 % 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: 2.93 (0.27), residues: 1018 helix: 2.23 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -0.21 (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 139 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: 1 63 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8233 (mm) REVERT: 7 69 PHE cc_start: 0.8646 (t80) cc_final: 0.8327 (t80) REVERT: d 27 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6699 (tpp-160) outliers start: 10 outliers final: 1 residues processed: 131 average time/residue: 1.0340 time to fit residues: 145.0790 Evaluate side-chains 111 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 3 residue 21 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 51 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 101 optimal weight: 0.0670 chunk 83 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 75 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7944 Z= 0.213 Angle : 0.557 7.826 10822 Z= 0.287 Chirality : 0.041 0.139 1248 Planarity : 0.004 0.047 1329 Dihedral : 9.270 150.700 1341 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.01 % Allowed : 10.89 % Favored : 87.11 % 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: 3.37 (0.27), residues: 1018 helix: 2.54 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -0.21 (0.66), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP a 208 HIS 0.003 0.001 HIS a 146 PHE 0.021 0.001 PHE a 142 TYR 0.037 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 145 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: 1 63 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8215 (mm) REVERT: 6 75 MET cc_start: 0.7844 (tmm) cc_final: 0.7455 (tmm) REVERT: 7 69 PHE cc_start: 0.8640 (t80) cc_final: 0.8370 (t80) REVERT: d 27 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6731 (tpp-160) outliers start: 14 outliers final: 3 residues processed: 135 average time/residue: 0.8994 time to fit residues: 130.9634 Evaluate side-chains 119 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 b residue 63 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 92 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** 5 46 GLN 6 46 GLN 9 50 GLN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1944 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= 0.249 Angle : 0.567 8.193 10822 Z= 0.292 Chirality : 0.042 0.151 1248 Planarity : 0.004 0.045 1329 Dihedral : 8.450 146.376 1341 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.15 % Allowed : 12.61 % Favored : 85.24 % 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: 3.24 (0.27), residues: 1018 helix: 2.46 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -0.30 (0.64), 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 0.002 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 140 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: 1 63 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8218 (mm) REVERT: 6 75 MET cc_start: 0.7920 (tmm) cc_final: 0.7480 (tmm) REVERT: 7 69 PHE cc_start: 0.8653 (t80) cc_final: 0.8343 (t80) REVERT: d 27 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6701 (tpp-160) outliers start: 15 outliers final: 3 residues processed: 129 average time/residue: 0.9943 time to fit residues: 137.9844 Evaluate side-chains 121 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 b residue 63 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 82 optimal weight: 0.0870 chunk 56 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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** 5 46 GLN 6 46 GLN 9 50 GLN a 112 GLN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7944 Z= 0.231 Angle : 0.562 8.570 10822 Z= 0.290 Chirality : 0.041 0.145 1248 Planarity : 0.004 0.045 1329 Dihedral : 7.869 140.372 1341 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.15 % Allowed : 13.04 % 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: 3.23 (0.26), residues: 1018 helix: 2.46 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -0.41 (0.62), 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 0.038 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 141 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: 1 63 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8201 (mm) REVERT: 6 75 MET cc_start: 0.7959 (tmm) cc_final: 0.7570 (tmm) REVERT: 7 69 PHE cc_start: 0.8627 (t80) cc_final: 0.8339 (t80) REVERT: d 27 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6728 (tpp-160) outliers start: 15 outliers final: 6 residues processed: 132 average time/residue: 1.0059 time to fit residues: 142.2984 Evaluate side-chains 125 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 8 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.0170 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- 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** 5 46 GLN 6 46 GLN 9 50 GLN 9 71 ASN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2131 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= 0.226 Angle : 0.563 9.479 10822 Z= 0.289 Chirality : 0.041 0.146 1248 Planarity : 0.004 0.049 1329 Dihedral : 7.415 135.394 1341 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.29 % Allowed : 13.04 % 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: 3.21 (0.26), residues: 1018 helix: 2.46 (0.17), residues: 894 sheet: -2.95 (1.58), residues: 9 loop : -0.22 (0.65), 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 0.018 0.001 PHE a 142 TYR 0.039 0.002 TYR a 145 ARG 0.008 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 140 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: 1 63 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8185 (mm) REVERT: 6 75 MET cc_start: 0.7944 (tmm) cc_final: 0.7525 (tmm) REVERT: 7 69 PHE cc_start: 0.8623 (t80) cc_final: 0.8309 (t80) REVERT: d 27 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6752 (tpp-160) outliers start: 16 outliers final: 6 residues processed: 128 average time/residue: 1.0008 time to fit residues: 137.3466 Evaluate side-chains 124 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 8 ILE 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 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 96 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 60 optimal weight: 0.0970 chunk 45 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7944 Z= 0.221 Angle : 0.573 10.073 10822 Z= 0.294 Chirality : 0.041 0.159 1248 Planarity : 0.004 0.044 1329 Dihedral : 7.092 129.828 1341 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.29 % Allowed : 14.18 % 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: 3.25 (0.26), residues: 1018 helix: 2.48 (0.17), residues: 895 sheet: -2.94 (1.58), residues: 9 loop : -0.19 (0.65), 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 0.019 0.001 PHE a 142 TYR 0.040 0.002 TYR a 145 ARG 0.008 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 138 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: 1 63 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8159 (mm) REVERT: 6 75 MET cc_start: 0.7952 (tmm) cc_final: 0.7481 (tmm) REVERT: 7 69 PHE cc_start: 0.8598 (t80) cc_final: 0.8296 (t80) REVERT: d 27 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6837 (tpp-160) outliers start: 16 outliers final: 7 residues processed: 126 average time/residue: 1.1511 time to fit residues: 155.0726 Evaluate side-chains 123 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 8 ILE Chi-restraints excluded: chain 3 residue 21 MET Chi-restraints excluded: chain 7 residue 8 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.0060 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7944 Z= 0.214 Angle : 0.572 10.814 10822 Z= 0.292 Chirality : 0.041 0.177 1248 Planarity : 0.004 0.043 1329 Dihedral : 6.888 123.015 1341 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.01 % Allowed : 14.18 % Favored : 83.81 % 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: 3.26 (0.26), residues: 1018 helix: 2.50 (0.17), residues: 895 sheet: -2.93 (1.58), residues: 9 loop : -0.26 (0.64), residues: 114 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 0.021 0.001 PHE 6 74 TYR 0.041 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 129 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: 6 75 MET cc_start: 0.7964 (tmm) cc_final: 0.7497 (tmm) REVERT: 7 69 PHE cc_start: 0.8596 (t80) cc_final: 0.8305 (t80) REVERT: d 27 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6921 (tpp-160) outliers start: 14 outliers final: 8 residues processed: 121 average time/residue: 1.0884 time to fit residues: 140.9563 Evaluate side-chains 121 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 8 ILE Chi-restraints excluded: chain 3 residue 21 MET Chi-restraints excluded: chain 7 residue 8 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7944 Z= 0.245 Angle : 0.602 11.480 10822 Z= 0.305 Chirality : 0.042 0.183 1248 Planarity : 0.005 0.079 1329 Dihedral : 6.849 116.499 1341 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.86 % Allowed : 14.90 % Favored : 83.24 % 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: 3.20 (0.26), residues: 1018 helix: 2.45 (0.17), residues: 895 sheet: -2.92 (1.59), residues: 9 loop : -0.24 (0.63), residues: 114 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 0.018 0.001 PHE a 142 TYR 0.041 0.002 TYR a 145 ARG 0.008 0.001 ARG a 74 *********************** 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 123 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: 1 63 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8153 (mm) REVERT: 6 75 MET cc_start: 0.7968 (tmm) cc_final: 0.7505 (tmm) REVERT: 7 69 PHE cc_start: 0.8602 (t80) cc_final: 0.8299 (t80) REVERT: 9 75 MET cc_start: 0.6522 (ttp) cc_final: 0.6315 (ttp) outliers start: 13 outliers final: 8 residues processed: 114 average time/residue: 1.0525 time to fit residues: 128.4588 Evaluate side-chains 117 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 8 ILE Chi-restraints excluded: chain 3 residue 21 MET Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 4 residue 77 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 8 optimal weight: 0.0980 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 87 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 6 ASN 9 50 GLN ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2373 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= 0.213 Angle : 0.599 12.626 10822 Z= 0.301 Chirality : 0.041 0.184 1248 Planarity : 0.005 0.067 1329 Dihedral : 6.627 108.317 1337 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.58 % Allowed : 15.33 % Favored : 83.09 % 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: 3.21 (0.26), residues: 1018 helix: 2.46 (0.17), residues: 895 sheet: -2.93 (1.59), residues: 9 loop : -0.30 (0.63), 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 0.023 0.001 PHE 6 74 TYR 0.041 0.002 TYR a 145 ARG 0.009 0.001 ARG 3 52 ********************** 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 123 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: 6 75 MET cc_start: 0.7926 (tmm) cc_final: 0.7521 (tmm) REVERT: 7 69 PHE cc_start: 0.8586 (t80) cc_final: 0.8293 (t80) REVERT: a 222 ASP cc_start: 0.7761 (t0) cc_final: 0.7446 (t0) outliers start: 11 outliers final: 7 residues processed: 116 average time/residue: 1.1026 time to fit residues: 136.7420 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 : 0.808 ------------------------------------------------------------------------------- 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 8 ILE Chi-restraints excluded: chain 4 residue 77 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 71 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.139303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117617 restraints weight = 6445.596| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.02 r_work: 0.3253 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7944 Z= 0.254 Angle : 0.636 12.620 10822 Z= 0.321 Chirality : 0.042 0.229 1248 Planarity : 0.005 0.066 1329 Dihedral : 6.632 99.394 1337 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.58 % Allowed : 15.62 % Favored : 82.81 % 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: 3.14 (0.26), residues: 1018 helix: 2.41 (0.17), residues: 895 sheet: -2.93 (1.59), residues: 9 loop : -0.24 (0.63), residues: 114 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 0.017 0.001 PHE a 142 TYR 0.008 0.001 TYR 8 68 ARG 0.009 0.001 ARG 3 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2779.50 seconds wall clock time: 50 minutes 35.72 seconds (3035.72 seconds total)