Starting phenix.real_space_refine on Fri Aug 22 19:38:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g07_29648/08_2025/8g07_29648.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g07_29648/08_2025/8g07_29648.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/8g07_29648/08_2025/8g07_29648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g07_29648/08_2025/8g07_29648.map" model { file = "/net/cci-nas-00/data/ceres_data/8g07_29648/08_2025/8g07_29648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g07_29648/08_2025/8g07_29648.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.169 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: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 4978 2.51 5 N 1212 2.21 5 O 1250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7467 Number of models: 1 Model: "" Number of chains: 13 Chain: "1" 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: "2" 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: "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: 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: "5" 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: "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: 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: "a" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1808 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "b" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 312 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 37} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "d" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 295 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 37} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "9" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'SQC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.22, per 1000 atoms: 0.30 Number of scatterers: 7467 At special positions: 0 Unit cell: (89.61, 76.22, 84.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1250 8.00 N 1212 7.00 C 4978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 491.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1758 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 88.4% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain '1' and resid 5 through 46 Processing helix chain '1' and resid 48 through 81 removed outlier: 4.269A pdb=" N ARG 1 52 " --> pdb=" O GLU 1 48 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE 1 54 " --> pdb=" O GLN 1 50 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR 1 55 " --> pdb=" O GLY 1 51 " (cutoff:3.500A) Proline residue: 1 56 - end of helix removed outlier: 3.763A pdb=" N ALA 1 67 " --> pdb=" O LEU 1 63 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR 1 68 " --> pdb=" O VAL 1 64 " (cutoff:3.500A) Processing helix chain '2' and resid 6 through 46 Processing helix chain '2' and resid 49 through 81 removed outlier: 4.394A 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: 4.410A pdb=" N THR 3 55 " --> pdb=" O GLY 3 51 " (cutoff:3.500A) Proline residue: 3 56 - end of helix Processing helix chain '4' and resid 6 through 46 Processing helix chain '4' and resid 49 through 81 removed outlier: 3.670A pdb=" N PHE 4 54 " --> pdb=" O GLN 4 50 " (cutoff:3.500A) removed outlier: 4.691A 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 80 removed outlier: 3.847A pdb=" N THR 5 55 " --> pdb=" O GLY 5 51 " (cutoff:3.500A) Proline residue: 5 56 - end of helix Processing helix chain '6' and resid 6 through 46 Processing helix chain '6' and resid 49 through 80 removed outlier: 4.501A pdb=" N THR 6 55 " --> pdb=" O GLY 6 51 " (cutoff:3.500A) Proline residue: 6 56 - end of helix Processing helix chain '7' and resid 6 through 46 Processing helix chain '7' and resid 48 through 80 removed outlier: 4.102A pdb=" N ARG 7 52 " --> pdb=" O GLU 7 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE 7 54 " --> pdb=" O GLN 7 50 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR 7 55 " --> pdb=" O GLY 7 51 " (cutoff:3.500A) Proline residue: 7 56 - end of helix Processing helix chain '8' and resid 6 through 46 Processing helix chain '8' and resid 49 through 80 removed outlier: 4.025A pdb=" N THR 8 55 " --> pdb=" O GLY 8 51 " (cutoff:3.500A) Proline residue: 8 56 - end of helix Processing helix chain '9' and resid 6 through 46 Processing helix chain '9' and resid 48 through 53 removed outlier: 4.205A pdb=" N ARG 9 52 " --> pdb=" O GLU 9 48 " (cutoff:3.500A) Processing helix chain '9' and resid 53 through 80 removed outlier: 3.775A pdb=" N ALA 9 67 " --> pdb=" O LEU 9 63 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR 9 68 " --> pdb=" O VAL 9 64 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE 9 80 " --> pdb=" O ALA 9 76 " (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: 3.576A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR a 95 " --> pdb=" O PRO a 91 " (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 Processing helix chain 'a' and resid 156 through 165 removed outlier: 3.745A pdb=" N ILE a 160 " --> pdb=" O VAL a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 170 through 204 removed outlier: 3.634A pdb=" N VAL a 176 " --> pdb=" O PRO a 172 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU a 177 " --> pdb=" O ILE a 173 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 3.828A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 245 removed outlier: 5.561A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix Processing helix chain 'b' and resid 29 through 49 Processing helix chain 'b' and resid 49 through 64 removed outlier: 3.565A pdb=" N LEU b 64 " --> pdb=" O ARG b 60 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 40 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 114 746 hydrogen bonds defined for protein. 2229 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: 1.41 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1165 1.28 - 1.41: 1918 1.41 - 1.54: 4487 1.54 - 1.68: 10 1.68 - 1.81: 53 Bond restraints: 7633 Sorted by residual: bond pdb=" C PHE a 221 " pdb=" O PHE a 221 " ideal model delta sigma weight residual 1.237 1.144 0.093 1.17e-02 7.31e+03 6.28e+01 bond pdb=" C ASN 5 6 " pdb=" O ASN 5 6 " ideal model delta sigma weight residual 1.237 1.146 0.091 1.17e-02 7.31e+03 6.03e+01 bond pdb=" C16 SQC 9 601 " pdb=" N17 SQC 9 601 " ideal model delta sigma weight residual 1.320 1.459 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" N GLN 4 46 " pdb=" CA GLN 4 46 " ideal model delta sigma weight residual 1.464 1.390 0.073 1.09e-02 8.42e+03 4.50e+01 bond pdb=" C ASN 4 6 " pdb=" O ASN 4 6 " ideal model delta sigma weight residual 1.237 1.159 0.078 1.17e-02 7.31e+03 4.45e+01 ... (remaining 7628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 10103 1.90 - 3.81: 210 3.81 - 5.71: 53 5.71 - 7.61: 10 7.61 - 9.51: 2 Bond angle restraints: 10378 Sorted by residual: angle pdb=" C GLN 6 46 " pdb=" N PRO 6 47 " pdb=" CA PRO 6 47 " ideal model delta sigma weight residual 119.84 111.35 8.49 1.25e+00 6.40e-01 4.61e+01 angle pdb=" N THR d 28 " pdb=" CA THR d 28 " pdb=" C THR d 28 " ideal model delta sigma weight residual 110.97 104.31 6.66 1.09e+00 8.42e-01 3.73e+01 angle pdb=" N ALA 9 66 " pdb=" CA ALA 9 66 " pdb=" C ALA 9 66 " ideal model delta sigma weight residual 110.97 104.55 6.42 1.09e+00 8.42e-01 3.46e+01 angle pdb=" N VAL d 26 " pdb=" CA VAL d 26 " pdb=" C VAL d 26 " ideal model delta sigma weight residual 110.62 104.79 5.83 1.02e+00 9.61e-01 3.27e+01 angle pdb=" C GLN 4 46 " pdb=" N PRO 4 47 " pdb=" CA PRO 4 47 " ideal model delta sigma weight residual 119.56 124.73 -5.17 1.02e+00 9.61e-01 2.57e+01 ... (remaining 10373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 3821 15.84 - 31.69: 372 31.69 - 47.53: 73 47.53 - 63.37: 26 63.37 - 79.22: 9 Dihedral angle restraints: 4301 sinusoidal: 1496 harmonic: 2805 Sorted by residual: dihedral pdb=" C ALA 9 66 " pdb=" N ALA 9 66 " pdb=" CA ALA 9 66 " pdb=" CB ALA 9 66 " ideal model delta harmonic sigma weight residual -122.60 -111.73 -10.87 0 2.50e+00 1.60e-01 1.89e+01 dihedral pdb=" CA PHE 9 80 " pdb=" C PHE 9 80 " pdb=" N ALA 9 81 " pdb=" CA ALA 9 81 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" N GLN 4 46 " pdb=" C GLN 4 46 " pdb=" CA GLN 4 46 " pdb=" CB GLN 4 46 " ideal model delta harmonic sigma weight residual 122.80 113.21 9.59 0 2.50e+00 1.60e-01 1.47e+01 ... (remaining 4298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 949 0.048 - 0.096: 241 0.096 - 0.144: 36 0.144 - 0.192: 8 0.192 - 0.240: 1 Chirality restraints: 1235 Sorted by residual: chirality pdb=" CB VAL 9 64 " pdb=" CA VAL 9 64 " pdb=" CG1 VAL 9 64 " pdb=" CG2 VAL 9 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA LEU 8 72 " pdb=" N LEU 8 72 " pdb=" C LEU 8 72 " pdb=" CB LEU 8 72 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CA PRO 6 47 " pdb=" N PRO 6 47 " pdb=" C PRO 6 47 " pdb=" CB PRO 6 47 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 1232 not shown) Planarity restraints: 1309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA 3 76 " 0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C ALA 3 76 " -0.065 2.00e-02 2.50e+03 pdb=" O ALA 3 76 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU 3 77 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY a 197 " -0.013 2.00e-02 2.50e+03 2.47e-02 6.11e+00 pdb=" C GLY a 197 " 0.043 2.00e-02 2.50e+03 pdb=" O GLY a 197 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE a 198 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE 4 69 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C PHE 4 69 " -0.042 2.00e-02 2.50e+03 pdb=" O PHE 4 69 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE 4 70 " 0.014 2.00e-02 2.50e+03 ... (remaining 1306 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1784 2.78 - 3.31: 8206 3.31 - 3.84: 13861 3.84 - 4.37: 16310 4.37 - 4.90: 28042 Nonbonded interactions: 68203 Sorted by model distance: nonbonded pdb=" OG SER a 55 " pdb=" OE1 GLU b 59 " model vdw 2.253 3.040 nonbonded pdb=" O GLN a 72 " pdb=" OE1 GLN a 76 " model vdw 2.299 3.040 nonbonded pdb=" O PHE a 99 " pdb=" OG SER a 103 " model vdw 2.304 3.040 nonbonded pdb=" OD1 ASP a 30 " pdb=" N THR a 31 " model vdw 2.314 3.120 nonbonded pdb=" O ALA 7 67 " pdb=" OD1 ASN 7 71 " model vdw 2.381 3.040 ... (remaining 68198 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 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 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 '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 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 '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 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 '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 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)) } 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: 2.210 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.760 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 0.139 7633 Z= 0.588 Angle : 0.715 9.513 10378 Z= 0.463 Chirality : 0.043 0.240 1235 Planarity : 0.005 0.057 1309 Dihedral : 13.982 79.219 2543 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.15 % Allowed : 2.31 % Favored : 96.54 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.27), residues: 1019 helix: 1.07 (0.18), residues: 843 sheet: -1.97 (1.47), residues: 9 loop : -0.67 (0.53), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 7 52 TYR 0.014 0.001 TYR a 145 PHE 0.012 0.001 PHE 6 74 TRP 0.007 0.001 TRP a 218 HIS 0.002 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00828 ( 7633) covalent geometry : angle 0.71486 (10378) hydrogen bonds : bond 0.14577 ( 746) hydrogen bonds : angle 7.30945 ( 2229) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.307 Fit side-chains REVERT: 4 21 MET cc_start: 0.7539 (mmm) cc_final: 0.7272 (mmm) REVERT: 4 45 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6860 (tmt170) REVERT: 7 58 PHE cc_start: 0.7971 (m-80) cc_final: 0.7706 (m-80) REVERT: a 73 MET cc_start: 0.7829 (mmt) cc_final: 0.7146 (mmt) REVERT: a 210 ILE cc_start: 0.7473 (mm) cc_final: 0.7261 (mm) outliers start: 8 outliers final: 0 residues processed: 125 average time/residue: 0.5564 time to fit residues: 73.7847 Evaluate side-chains 92 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 45 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 6 ASN 7 46 GLN ** 7 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 46 GLN 9 50 GLN ** a 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.132222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.109554 restraints weight = 8752.036| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.56 r_work: 0.3243 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7633 Z= 0.216 Angle : 0.592 6.417 10378 Z= 0.318 Chirality : 0.043 0.165 1235 Planarity : 0.005 0.042 1309 Dihedral : 5.706 60.490 1110 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.45 % Allowed : 9.80 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.89 (0.26), residues: 1019 helix: 2.27 (0.17), residues: 844 sheet: -1.84 (1.51), residues: 9 loop : 0.34 (0.52), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 1 52 TYR 0.025 0.001 TYR a 145 PHE 0.024 0.002 PHE 6 74 TRP 0.020 0.002 TRP b 48 HIS 0.004 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 7633) covalent geometry : angle 0.59239 (10378) hydrogen bonds : bond 0.05224 ( 746) hydrogen bonds : angle 4.76757 ( 2229) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 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: 17 poor density : 106 time to evaluate : 0.273 Fit side-chains REVERT: 2 75 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8093 (tmm) REVERT: 4 45 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.6713 (tpt90) REVERT: a 73 MET cc_start: 0.8501 (mmt) cc_final: 0.7806 (mmt) REVERT: a 75 GLN cc_start: 0.8062 (mt0) cc_final: 0.7795 (mt0) REVERT: a 208 TRP cc_start: 0.8051 (p-90) cc_final: 0.7820 (p-90) outliers start: 17 outliers final: 6 residues processed: 116 average time/residue: 0.5739 time to fit residues: 70.4737 Evaluate side-chains 103 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 MET Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 6 residue 8 ILE Chi-restraints excluded: chain 8 residue 6 ASN Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain b residue 64 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 71 ASN 7 6 ASN 7 46 GLN 9 50 GLN a 63 GLN a 215 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.132959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110440 restraints weight = 8694.471| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.57 r_work: 0.3253 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7633 Z= 0.175 Angle : 0.541 6.480 10378 Z= 0.289 Chirality : 0.040 0.149 1235 Planarity : 0.004 0.043 1309 Dihedral : 5.600 64.539 1110 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.88 % Allowed : 12.54 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.31 (0.26), residues: 1019 helix: 2.57 (0.17), residues: 844 sheet: -1.83 (1.52), residues: 9 loop : 0.40 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 52 TYR 0.024 0.001 TYR a 145 PHE 0.020 0.002 PHE a 194 TRP 0.018 0.002 TRP b 48 HIS 0.003 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 7633) covalent geometry : angle 0.54144 (10378) hydrogen bonds : bond 0.04756 ( 746) hydrogen bonds : angle 4.51112 ( 2229) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 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: 20 poor density : 109 time to evaluate : 0.287 Fit side-chains REVERT: 2 45 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7904 (mtp-110) REVERT: 2 75 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8147 (tmm) REVERT: 4 45 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6612 (tpt90) REVERT: 5 52 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7135 (mtm180) REVERT: 6 74 PHE cc_start: 0.8318 (m-80) cc_final: 0.8038 (m-80) REVERT: 7 52 ARG cc_start: 0.8056 (ptt-90) cc_final: 0.7837 (ptt-90) REVERT: a 73 MET cc_start: 0.8443 (mmt) cc_final: 0.7573 (mmt) REVERT: a 76 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7414 (mp10) REVERT: a 210 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7460 (tp) REVERT: d 5 ILE cc_start: 0.7850 (mm) cc_final: 0.7586 (mp) outliers start: 20 outliers final: 6 residues processed: 121 average time/residue: 0.5731 time to fit residues: 73.4054 Evaluate side-chains 112 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 45 ARG Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 52 ARG Chi-restraints excluded: chain 8 residue 6 ASN Chi-restraints excluded: chain 9 residue 21 MET Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 210 ILE Chi-restraints excluded: chain a residue 215 ASN Chi-restraints excluded: chain b residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 11 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 6 ASN 7 46 GLN 9 50 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 215 ASN a 229 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.133648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111019 restraints weight = 8783.864| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.57 r_work: 0.3259 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7633 Z= 0.168 Angle : 0.533 6.514 10378 Z= 0.283 Chirality : 0.040 0.161 1235 Planarity : 0.004 0.043 1309 Dihedral : 5.572 66.557 1110 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.60 % Allowed : 12.25 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.43 (0.26), residues: 1019 helix: 2.66 (0.17), residues: 844 sheet: -1.93 (1.47), residues: 9 loop : 0.43 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 1 52 TYR 0.023 0.001 TYR a 145 PHE 0.017 0.002 PHE a 194 TRP 0.017 0.002 TRP b 48 HIS 0.003 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 7633) covalent geometry : angle 0.53284 (10378) hydrogen bonds : bond 0.04629 ( 746) hydrogen bonds : angle 4.44170 ( 2229) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.276 Fit side-chains REVERT: 2 21 MET cc_start: 0.8488 (mmm) cc_final: 0.8228 (mmm) REVERT: 2 45 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7788 (mtp-110) REVERT: 4 45 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6608 (tpt90) REVERT: 4 68 TYR cc_start: 0.8726 (t80) cc_final: 0.8477 (t80) REVERT: 5 45 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6883 (ptm160) REVERT: 5 52 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7157 (mtm180) REVERT: 6 74 PHE cc_start: 0.8344 (m-80) cc_final: 0.8082 (m-80) REVERT: a 50 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6510 (ttm170) REVERT: a 73 MET cc_start: 0.8418 (mmt) cc_final: 0.7550 (mmt) REVERT: a 76 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7329 (mp10) REVERT: a 210 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7389 (tp) REVERT: d 1 MET cc_start: 0.7565 (tpp) cc_final: 0.7173 (tpp) REVERT: d 5 ILE cc_start: 0.7819 (mm) cc_final: 0.7556 (mp) REVERT: d 27 ARG cc_start: 0.6420 (OUTLIER) cc_final: 0.6051 (ttm-80) outliers start: 25 outliers final: 6 residues processed: 120 average time/residue: 0.6240 time to fit residues: 79.0100 Evaluate side-chains 113 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 45 ARG Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 5 residue 52 ARG Chi-restraints excluded: chain 9 residue 21 MET Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 210 ILE Chi-restraints excluded: chain a residue 215 ASN Chi-restraints excluded: chain b residue 64 LEU 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 69 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN 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 = 0.132856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110154 restraints weight = 8772.881| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.56 r_work: 0.3253 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7633 Z= 0.175 Angle : 0.528 6.534 10378 Z= 0.282 Chirality : 0.040 0.180 1235 Planarity : 0.004 0.043 1309 Dihedral : 5.600 68.816 1110 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.17 % Allowed : 13.11 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.42 (0.26), residues: 1019 helix: 2.67 (0.17), residues: 843 sheet: -2.12 (1.40), residues: 9 loop : 0.33 (0.50), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 1 52 TYR 0.023 0.001 TYR a 145 PHE 0.020 0.002 PHE 1 69 TRP 0.016 0.001 TRP b 48 HIS 0.003 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 7633) covalent geometry : angle 0.52842 (10378) hydrogen bonds : bond 0.04604 ( 746) hydrogen bonds : angle 4.42188 ( 2229) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.267 Fit side-chains REVERT: 2 21 MET cc_start: 0.8483 (mmm) cc_final: 0.8130 (mmm) REVERT: 2 45 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7869 (mtp-110) REVERT: 2 75 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8216 (tmm) REVERT: 4 45 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6593 (tpt90) REVERT: 5 45 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6964 (ptm160) REVERT: 5 52 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7161 (mtm180) REVERT: 6 74 PHE cc_start: 0.8430 (m-80) cc_final: 0.8119 (m-80) REVERT: 7 85 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7512 (mp) REVERT: a 50 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6508 (ttm170) REVERT: a 73 MET cc_start: 0.8443 (mmt) cc_final: 0.7584 (mmt) REVERT: a 76 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7396 (mp10) REVERT: a 210 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7360 (tp) REVERT: d 1 MET cc_start: 0.7567 (tpp) cc_final: 0.7162 (tpp) REVERT: d 5 ILE cc_start: 0.7805 (mm) cc_final: 0.7533 (mp) REVERT: d 27 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6391 (ttm-80) outliers start: 22 outliers final: 6 residues processed: 113 average time/residue: 0.6132 time to fit residues: 73.2259 Evaluate side-chains 113 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 45 ARG Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 3 residue 21 MET Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 5 residue 52 ARG Chi-restraints excluded: chain 7 residue 85 LEU Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain a residue 210 ILE Chi-restraints excluded: chain a residue 215 ASN Chi-restraints excluded: chain b residue 64 LEU 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 57 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.133107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.110421 restraints weight = 8733.085| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.56 r_work: 0.3254 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7633 Z= 0.171 Angle : 0.528 6.534 10378 Z= 0.281 Chirality : 0.040 0.155 1235 Planarity : 0.004 0.044 1309 Dihedral : 5.602 70.531 1110 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 4.03 % Allowed : 12.97 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.46 (0.26), residues: 1019 helix: 2.70 (0.17), residues: 843 sheet: -2.12 (1.40), residues: 9 loop : 0.32 (0.50), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 1 52 TYR 0.023 0.001 TYR a 145 PHE 0.020 0.002 PHE 1 69 TRP 0.017 0.001 TRP b 48 HIS 0.003 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 7633) covalent geometry : angle 0.52837 (10378) hydrogen bonds : bond 0.04568 ( 746) hydrogen bonds : angle 4.40511 ( 2229) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.287 Fit side-chains REVERT: 2 21 MET cc_start: 0.8521 (mmm) cc_final: 0.7921 (tpt) REVERT: 2 45 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7895 (mtp-110) REVERT: 2 75 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8158 (tmm) REVERT: 4 45 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6581 (tpt90) REVERT: 5 45 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6966 (ptm160) REVERT: 5 52 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7182 (mtm180) REVERT: 6 45 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7714 (ttp-110) REVERT: 6 74 PHE cc_start: 0.8447 (m-80) cc_final: 0.8046 (m-80) REVERT: 7 85 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7497 (mp) REVERT: a 50 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6510 (ttm170) REVERT: a 73 MET cc_start: 0.8455 (mmt) cc_final: 0.7596 (mmt) REVERT: a 76 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7380 (mp10) REVERT: a 210 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7282 (tp) REVERT: d 1 MET cc_start: 0.7583 (tpp) cc_final: 0.7221 (tpt) REVERT: d 5 ILE cc_start: 0.7791 (mm) cc_final: 0.7524 (mp) outliers start: 28 outliers final: 8 residues processed: 118 average time/residue: 0.5742 time to fit residues: 71.8193 Evaluate side-chains 115 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 45 ARG Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 5 residue 52 ARG Chi-restraints excluded: chain 6 residue 54 PHE Chi-restraints excluded: chain 6 residue 72 LEU Chi-restraints excluded: chain 7 residue 85 LEU Chi-restraints excluded: chain 8 residue 6 ASN Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain a residue 210 ILE Chi-restraints excluded: chain a residue 215 ASN Chi-restraints excluded: chain b residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 15 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN 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 = 0.133293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.110503 restraints weight = 8786.635| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.57 r_work: 0.3255 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7633 Z= 0.169 Angle : 0.533 6.944 10378 Z= 0.283 Chirality : 0.040 0.182 1235 Planarity : 0.004 0.043 1309 Dihedral : 5.599 71.543 1110 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.89 % Allowed : 13.83 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.48 (0.26), residues: 1019 helix: 2.72 (0.17), residues: 843 sheet: -2.13 (1.40), residues: 9 loop : 0.30 (0.49), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 1 52 TYR 0.023 0.001 TYR a 145 PHE 0.019 0.002 PHE 1 69 TRP 0.019 0.001 TRP b 48 HIS 0.005 0.001 HIS a 16 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 7633) covalent geometry : angle 0.53280 (10378) hydrogen bonds : bond 0.04547 ( 746) hydrogen bonds : angle 4.39842 ( 2229) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 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: 27 poor density : 102 time to evaluate : 0.272 Fit side-chains REVERT: 2 21 MET cc_start: 0.8521 (mmm) cc_final: 0.7928 (tpt) REVERT: 2 45 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7866 (mtp-110) REVERT: 2 75 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8090 (tmm) REVERT: 4 45 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6577 (tpt90) REVERT: 5 45 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6917 (ptm160) REVERT: 5 52 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7194 (mtm180) REVERT: 6 74 PHE cc_start: 0.8406 (m-80) cc_final: 0.8058 (m-80) REVERT: 6 75 MET cc_start: 0.8022 (ttp) cc_final: 0.7551 (ttt) REVERT: 7 85 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7424 (mp) REVERT: a 50 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6517 (ttm170) REVERT: a 73 MET cc_start: 0.8449 (mmt) cc_final: 0.7595 (mmt) REVERT: a 76 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7386 (mp10) REVERT: a 210 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7262 (tp) REVERT: d 1 MET cc_start: 0.7609 (tpp) cc_final: 0.7254 (tpt) REVERT: d 5 ILE cc_start: 0.7812 (mm) cc_final: 0.7546 (mp) outliers start: 27 outliers final: 9 residues processed: 117 average time/residue: 0.6196 time to fit residues: 76.5906 Evaluate side-chains 116 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 45 ARG Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 5 residue 52 ARG Chi-restraints excluded: chain 6 residue 54 PHE Chi-restraints excluded: chain 6 residue 72 LEU Chi-restraints excluded: chain 7 residue 85 LEU Chi-restraints excluded: chain 8 residue 85 LEU Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain a residue 210 ILE Chi-restraints excluded: chain a residue 215 ASN Chi-restraints excluded: chain b residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 2 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.132126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.109270 restraints weight = 8860.387| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.57 r_work: 0.3239 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7633 Z= 0.200 Angle : 0.556 8.137 10378 Z= 0.295 Chirality : 0.041 0.178 1235 Planarity : 0.005 0.062 1309 Dihedral : 5.711 73.026 1110 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.46 % Allowed : 14.84 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.35 (0.26), residues: 1019 helix: 2.63 (0.17), residues: 843 sheet: -2.23 (1.37), residues: 9 loop : 0.27 (0.48), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 1 52 TYR 0.023 0.001 TYR a 145 PHE 0.020 0.002 PHE 1 69 TRP 0.023 0.002 TRP b 48 HIS 0.005 0.001 HIS a 16 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 7633) covalent geometry : angle 0.55630 (10378) hydrogen bonds : bond 0.04672 ( 746) hydrogen bonds : angle 4.46168 ( 2229) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.333 Fit side-chains REVERT: 2 21 MET cc_start: 0.8546 (mmm) cc_final: 0.7964 (tpt) REVERT: 2 45 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7909 (mtp-110) REVERT: 2 75 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8163 (tmm) REVERT: 4 45 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.6553 (tpt90) REVERT: 5 45 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6942 (ptm160) REVERT: 5 52 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7232 (mtm180) REVERT: 6 74 PHE cc_start: 0.8427 (m-80) cc_final: 0.8163 (m-80) REVERT: a 50 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6599 (ttm170) REVERT: a 73 MET cc_start: 0.8489 (mmt) cc_final: 0.7709 (mmt) REVERT: a 76 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7399 (mp10) REVERT: a 210 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7232 (tp) REVERT: d 1 MET cc_start: 0.7660 (tpp) cc_final: 0.7309 (tpt) REVERT: d 5 ILE cc_start: 0.7811 (mm) cc_final: 0.7537 (mp) outliers start: 24 outliers final: 8 residues processed: 114 average time/residue: 0.6027 time to fit residues: 72.6476 Evaluate side-chains 115 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 45 ARG Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 5 residue 52 ARG Chi-restraints excluded: chain 6 residue 54 PHE Chi-restraints excluded: chain 8 residue 85 LEU Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain a residue 210 ILE Chi-restraints excluded: chain a residue 215 ASN Chi-restraints excluded: chain b residue 64 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.133403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.110962 restraints weight = 8720.013| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.55 r_work: 0.3261 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7633 Z= 0.167 Angle : 0.543 7.605 10378 Z= 0.288 Chirality : 0.040 0.164 1235 Planarity : 0.005 0.059 1309 Dihedral : 5.648 73.374 1110 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.03 % Allowed : 14.84 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.41 (0.26), residues: 1019 helix: 2.68 (0.17), residues: 843 sheet: -2.08 (1.40), residues: 9 loop : 0.22 (0.48), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 1 52 TYR 0.022 0.001 TYR a 145 PHE 0.020 0.002 PHE 4 74 TRP 0.024 0.002 TRP b 48 HIS 0.004 0.001 HIS a 16 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 7633) covalent geometry : angle 0.54336 (10378) hydrogen bonds : bond 0.04555 ( 746) hydrogen bonds : angle 4.42330 ( 2229) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.170 Fit side-chains REVERT: 2 21 MET cc_start: 0.8494 (mmm) cc_final: 0.7930 (tpt) REVERT: 2 45 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7925 (mtp-110) REVERT: 2 75 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8073 (tmm) REVERT: 4 45 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6617 (tpt90) REVERT: 5 45 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6931 (ptm160) REVERT: 6 74 PHE cc_start: 0.8376 (m-80) cc_final: 0.8103 (m-80) REVERT: 6 75 MET cc_start: 0.8020 (ttp) cc_final: 0.7616 (ttt) REVERT: a 50 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6582 (ttm170) REVERT: a 73 MET cc_start: 0.8460 (mmt) cc_final: 0.7616 (mmt) REVERT: a 76 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7362 (mp10) REVERT: a 210 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7129 (tp) REVERT: d 1 MET cc_start: 0.7688 (tpp) cc_final: 0.7356 (tpt) REVERT: d 5 ILE cc_start: 0.7789 (mm) cc_final: 0.7527 (mp) outliers start: 21 outliers final: 9 residues processed: 112 average time/residue: 0.5308 time to fit residues: 62.8606 Evaluate side-chains 113 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 45 ARG Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 6 residue 54 PHE Chi-restraints excluded: chain 8 residue 85 LEU Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain a residue 210 ILE Chi-restraints excluded: chain a residue 215 ASN Chi-restraints excluded: chain b residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 98 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 91 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.134285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.111846 restraints weight = 8801.410| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.55 r_work: 0.3272 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7633 Z= 0.160 Angle : 0.551 9.021 10378 Z= 0.289 Chirality : 0.040 0.156 1235 Planarity : 0.004 0.042 1309 Dihedral : 5.598 72.745 1110 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.74 % Allowed : 15.13 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.46 (0.26), residues: 1019 helix: 2.72 (0.17), residues: 843 sheet: -2.10 (1.40), residues: 9 loop : 0.23 (0.49), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 52 TYR 0.022 0.001 TYR a 145 PHE 0.027 0.002 PHE 6 74 TRP 0.027 0.002 TRP b 48 HIS 0.004 0.001 HIS a 16 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 7633) covalent geometry : angle 0.55101 (10378) hydrogen bonds : bond 0.04502 ( 746) hydrogen bonds : angle 4.40434 ( 2229) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.172 Fit side-chains REVERT: 2 21 MET cc_start: 0.8470 (mmm) cc_final: 0.7907 (tpt) REVERT: 2 75 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8014 (tmm) REVERT: 4 45 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.6631 (tpt90) REVERT: 5 45 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6964 (ptm160) REVERT: 6 75 MET cc_start: 0.8005 (ttp) cc_final: 0.7622 (ttt) REVERT: a 50 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6575 (ttm170) REVERT: a 73 MET cc_start: 0.8441 (mmt) cc_final: 0.7611 (mmt) REVERT: a 76 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7364 (mp10) REVERT: a 210 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7109 (tp) REVERT: d 1 MET cc_start: 0.7701 (tpp) cc_final: 0.7373 (tpt) REVERT: d 5 ILE cc_start: 0.7778 (mm) cc_final: 0.7518 (mp) outliers start: 19 outliers final: 8 residues processed: 112 average time/residue: 0.6034 time to fit residues: 71.1930 Evaluate side-chains 111 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 75 MET Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain 4 residue 45 ARG Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 8 residue 85 LEU Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 50 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 76 GLN Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain a residue 198 ILE Chi-restraints excluded: chain a residue 210 ILE Chi-restraints excluded: chain a residue 215 ASN Chi-restraints excluded: chain b residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 GLN ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 192 ASN a 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.111539 restraints weight = 8818.674| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.56 r_work: 0.3268 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7633 Z= 0.171 Angle : 0.581 17.310 10378 Z= 0.299 Chirality : 0.040 0.155 1235 Planarity : 0.004 0.042 1309 Dihedral : 5.620 72.707 1110 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.45 % Allowed : 15.99 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.46 (0.26), residues: 1019 helix: 2.72 (0.17), residues: 843 sheet: -2.11 (1.40), residues: 9 loop : 0.22 (0.48), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 2 45 TYR 0.022 0.001 TYR a 145 PHE 0.023 0.002 PHE 4 74 TRP 0.028 0.002 TRP b 48 HIS 0.004 0.001 HIS a 16 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 7633) covalent geometry : angle 0.58108 (10378) hydrogen bonds : bond 0.04521 ( 746) hydrogen bonds : angle 4.41777 ( 2229) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2550.11 seconds wall clock time: 44 minutes 19.18 seconds (2659.18 seconds total)