Starting phenix.real_space_refine on Wed Feb 12 07:54:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g0b_29652/02_2025/8g0b_29652.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g0b_29652/02_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_29652/02_2025/8g0b_29652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g0b_29652/02_2025/8g0b_29652.map" model { file = "/net/cci-nas-00/data/ceres_data/8g0b_29652/02_2025/8g0b_29652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g0b_29652/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.40, per 1000 atoms: 0.70 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: 1.94 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: 0.58 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: 2.46 Time building geometry restraints manager: 2.21 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: 1.300 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.240 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.050 ------------------------------------------------------------------------------- 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 : 0.811 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: 0.9780 time to fit residues: 145.5622 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 : 0.782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.139003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117681 restraints weight = 6397.245| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.02 r_work: 0.3259 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 0.749 Fit side-chains revert: symmetry clash REVERT: 1 63 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8184 (mm) REVERT: 7 69 PHE cc_start: 0.8609 (t80) cc_final: 0.8262 (t80) REVERT: a 205 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8206 (mtp) REVERT: d 27 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6468 (tpp-160) outliers start: 10 outliers final: 1 residues processed: 131 average time/residue: 1.0618 time to fit residues: 149.3172 Evaluate side-chains 112 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 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: 0.0470 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.139223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117704 restraints weight = 6487.187| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.02 r_work: 0.3263 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1799 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= 0.220 Angle : 0.559 7.896 10822 Z= 0.289 Chirality : 0.041 0.141 1248 Planarity : 0.004 0.047 1329 Dihedral : 9.312 151.162 1341 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.15 % Allowed : 10.74 % 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: 3.34 (0.27), residues: 1018 helix: 2.52 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -0.19 (0.67), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 208 HIS 0.002 0.001 HIS a 146 PHE 0.021 0.001 PHE a 142 TYR 0.035 0.002 TYR a 145 ARG 0.008 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 : 0.743 Fit side-chains revert: symmetry clash REVERT: 1 63 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8171 (mm) REVERT: 3 8 ILE cc_start: 0.9070 (mp) cc_final: 0.8761 (tt) REVERT: 6 75 MET cc_start: 0.8368 (tmm) cc_final: 0.7871 (tmm) REVERT: 7 69 PHE cc_start: 0.8618 (t80) cc_final: 0.8306 (t80) REVERT: a 205 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8121 (mtp) REVERT: d 27 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6572 (tpp-160) outliers start: 15 outliers final: 3 residues processed: 133 average time/residue: 0.9634 time to fit residues: 137.6703 Evaluate side-chains 119 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 47 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 72 optimal weight: 0.0770 chunk 20 optimal weight: 0.0770 chunk 11 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.140817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.119533 restraints weight = 6501.371| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.02 r_work: 0.3289 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7944 Z= 0.201 Angle : 0.544 7.723 10822 Z= 0.280 Chirality : 0.041 0.143 1248 Planarity : 0.004 0.044 1329 Dihedral : 8.217 143.771 1341 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.15 % Allowed : 12.18 % Favored : 85.67 % 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: 3.39 (0.27), residues: 1018 helix: 2.56 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -0.31 (0.63), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 208 HIS 0.003 0.001 HIS a 146 PHE 0.020 0.001 PHE a 142 TYR 0.035 0.002 TYR a 145 ARG 0.007 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 141 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: 3 8 ILE cc_start: 0.8984 (mp) cc_final: 0.8719 (tt) REVERT: 6 75 MET cc_start: 0.8416 (tmm) cc_final: 0.7902 (tmm) REVERT: 7 69 PHE cc_start: 0.8582 (t80) cc_final: 0.8254 (t80) REVERT: d 27 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6570 (tpp-160) outliers start: 15 outliers final: 4 residues processed: 130 average time/residue: 0.9793 time to fit residues: 136.6615 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 : 0.778 ------------------------------------------------------------------------------- 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 20 optimal weight: 0.3980 chunk 76 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.116739 restraints weight = 6453.262| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.02 r_work: 0.3252 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7944 Z= 0.250 Angle : 0.568 8.923 10822 Z= 0.292 Chirality : 0.041 0.147 1248 Planarity : 0.004 0.044 1329 Dihedral : 7.767 139.981 1341 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.58 % Allowed : 13.32 % Favored : 85.10 % 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: 3.31 (0.26), residues: 1018 helix: 2.52 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -0.43 (0.62), residues: 124 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 0.018 0.002 PHE a 142 TYR 0.037 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 134 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: 1 63 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8128 (mm) REVERT: 3 8 ILE cc_start: 0.8937 (mp) cc_final: 0.8682 (tt) REVERT: 6 75 MET cc_start: 0.8437 (tmm) cc_final: 0.7854 (tmm) REVERT: 7 69 PHE cc_start: 0.8561 (t80) cc_final: 0.8216 (t80) REVERT: a 246 GLU cc_start: 0.8111 (tp30) cc_final: 0.7857 (tp30) REVERT: d 27 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6537 (tpp-160) outliers start: 11 outliers final: 4 residues processed: 127 average time/residue: 1.0059 time to fit residues: 136.9711 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 : 0.744 ------------------------------------------------------------------------------- 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: 0.9980 chunk 78 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 0.0170 chunk 62 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 9 50 GLN a 112 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 = 0.3659 r_free = 0.3659 target = 0.140876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119486 restraints weight = 6497.279| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.02 r_work: 0.3289 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2235 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= 0.198 Angle : 0.549 9.214 10822 Z= 0.280 Chirality : 0.040 0.143 1248 Planarity : 0.004 0.044 1329 Dihedral : 7.252 133.037 1341 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.86 % Allowed : 13.61 % Favored : 84.53 % 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: 3.38 (0.26), residues: 1018 helix: 2.58 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -0.52 (0.61), 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 146 PHE 0.019 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 135 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.730 Fit side-chains REVERT: 3 8 ILE cc_start: 0.8890 (mp) cc_final: 0.8680 (tt) REVERT: 6 75 MET cc_start: 0.8447 (tmm) cc_final: 0.7935 (tmm) REVERT: 7 69 PHE cc_start: 0.8547 (t80) cc_final: 0.8202 (t80) REVERT: a 222 ASP cc_start: 0.8185 (t0) cc_final: 0.7850 (t0) REVERT: d 27 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6565 (tpp-160) outliers start: 13 outliers final: 6 residues processed: 127 average time/residue: 1.0265 time to fit residues: 139.4296 Evaluate side-chains 120 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 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 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 = 0.3649 r_free = 0.3649 target = 0.139892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118227 restraints weight = 6535.791| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.03 r_work: 0.3272 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2253 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= 0.226 Angle : 0.575 10.099 10822 Z= 0.294 Chirality : 0.041 0.147 1248 Planarity : 0.004 0.052 1329 Dihedral : 6.993 128.170 1341 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.15 % Allowed : 13.75 % Favored : 84.10 % 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 (0.26), residues: 1018 helix: 2.57 (0.17), residues: 895 sheet: -2.90 (1.59), residues: 9 loop : -0.41 (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 0.040 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 134 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.782 Fit side-chains REVERT: 3 8 ILE cc_start: 0.8890 (mp) cc_final: 0.8674 (tt) REVERT: 6 75 MET cc_start: 0.8442 (tmm) cc_final: 0.7890 (tmm) REVERT: 7 69 PHE cc_start: 0.8561 (t80) cc_final: 0.8224 (t80) REVERT: a 222 ASP cc_start: 0.8127 (t0) cc_final: 0.7798 (t0) REVERT: d 27 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6636 (tpp-160) outliers start: 15 outliers final: 6 residues processed: 123 average time/residue: 1.0008 time to fit residues: 132.0755 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 : 0.815 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 48 optimal weight: 7.9990 chunk 76 optimal weight: 0.0060 chunk 77 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.140280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118806 restraints weight = 6587.202| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.03 r_work: 0.3276 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7944 Z= 0.217 Angle : 0.575 10.638 10822 Z= 0.293 Chirality : 0.041 0.152 1248 Planarity : 0.005 0.070 1329 Dihedral : 6.836 121.121 1341 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.15 % Allowed : 14.18 % Favored : 83.67 % 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: 3.31 (0.26), residues: 1018 helix: 2.55 (0.17), residues: 895 sheet: -2.91 (1.59), residues: 9 loop : -0.49 (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 0.019 0.001 PHE 6 74 TYR 0.040 0.002 TYR a 145 ARG 0.009 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 135 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.812 Fit side-chains REVERT: 3 8 ILE cc_start: 0.8898 (mp) cc_final: 0.8676 (tt) REVERT: 6 75 MET cc_start: 0.8423 (tmm) cc_final: 0.7843 (tmm) REVERT: 7 69 PHE cc_start: 0.8552 (t80) cc_final: 0.8219 (t80) REVERT: a 222 ASP cc_start: 0.8120 (t0) cc_final: 0.7797 (t0) REVERT: d 27 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.6791 (tpp-160) outliers start: 15 outliers final: 7 residues processed: 128 average time/residue: 0.9780 time to fit residues: 134.6797 Evaluate side-chains 120 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 77 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 45 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.139021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117294 restraints weight = 6579.831| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.03 r_work: 0.3257 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7944 Z= 0.244 Angle : 0.609 11.416 10822 Z= 0.307 Chirality : 0.042 0.189 1248 Planarity : 0.005 0.063 1329 Dihedral : 6.802 113.933 1341 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.43 % Allowed : 15.04 % 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: 3.24 (0.26), residues: 1018 helix: 2.51 (0.17), residues: 895 sheet: -2.92 (1.59), residues: 9 loop : -0.53 (0.62), 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 0.017 0.002 PHE a 142 TYR 0.041 0.002 TYR a 145 ARG 0.012 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 120 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 1.095 Fit side-chains REVERT: 3 8 ILE cc_start: 0.8912 (mp) cc_final: 0.8684 (tt) REVERT: 6 75 MET cc_start: 0.8490 (tmm) cc_final: 0.7908 (tmm) REVERT: 7 69 PHE cc_start: 0.8571 (t80) cc_final: 0.8229 (t80) REVERT: a 222 ASP cc_start: 0.8140 (t0) cc_final: 0.7804 (t0) REVERT: d 27 ARG cc_start: 0.7543 (ttt90) cc_final: 0.6789 (tpp-160) outliers start: 10 outliers final: 7 residues processed: 115 average time/residue: 0.9687 time to fit residues: 119.7463 Evaluate side-chains 115 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 77 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 83 optimal weight: 0.2980 chunk 56 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 76 optimal weight: 0.0980 chunk 31 optimal weight: 0.0000 chunk 12 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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 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 = 0.3682 r_free = 0.3682 target = 0.142993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121593 restraints weight = 6573.929| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.02 r_work: 0.3312 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2502 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= 0.188 Angle : 0.578 12.010 10822 Z= 0.291 Chirality : 0.041 0.192 1248 Planarity : 0.005 0.054 1329 Dihedral : 6.528 100.168 1337 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.00 % Allowed : 16.05 % Favored : 82.95 % 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: 3.38 (0.26), residues: 1018 helix: 2.61 (0.17), residues: 895 sheet: -2.95 (1.56), residues: 9 loop : -0.57 (0.61), 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 0.018 0.001 PHE a 142 TYR 0.039 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 124 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.799 Fit side-chains REVERT: 6 75 MET cc_start: 0.8457 (tmm) cc_final: 0.7855 (tmm) REVERT: 7 69 PHE cc_start: 0.8527 (t80) cc_final: 0.8217 (t80) REVERT: d 27 ARG cc_start: 0.7552 (ttt90) cc_final: 0.6790 (tpp-160) outliers start: 7 outliers final: 4 residues processed: 121 average time/residue: 0.9363 time to fit residues: 122.0759 Evaluate side-chains 110 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 77 LEU 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: 0.7980 chunk 88 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 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 ** d 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.140712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118997 restraints weight = 6516.163| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.03 r_work: 0.3276 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2452 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= 0.241 Angle : 0.628 12.628 10822 Z= 0.315 Chirality : 0.042 0.228 1248 Planarity : 0.005 0.056 1329 Dihedral : 6.506 88.044 1337 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.86 % Allowed : 16.33 % 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: 3.28 (0.26), residues: 1018 helix: 2.53 (0.17), residues: 895 sheet: -2.90 (1.59), residues: 9 loop : -0.54 (0.61), 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 0.016 0.001 PHE a 142 TYR 0.009 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: 4855.80 seconds wall clock time: 86 minutes 25.16 seconds (5185.16 seconds total)