Starting phenix.real_space_refine on Tue Mar 3 17:17:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jgc_22321/03_2026/7jgc_22321.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jgc_22321/03_2026/7jgc_22321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jgc_22321/03_2026/7jgc_22321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jgc_22321/03_2026/7jgc_22321.map" model { file = "/net/cci-nas-00/data/ceres_data/7jgc_22321/03_2026/7jgc_22321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jgc_22321/03_2026/7jgc_22321.cif" } resolution = 3.4 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= 0.007 sd= 0.272 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 5067 2.51 5 N 1189 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7521 Number of models: 1 Model: "" Number of chains: 19 Chain: "a" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1594 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "b" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 319 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 37} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 37} 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: "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: 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: "3" 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: "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: 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: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "7" 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: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "8" 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: "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: "1" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'BQ1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.69, per 1000 atoms: 0.22 Number of scatterers: 7521 At special positions: 0 Unit cell: (78.28, 99.91, 84.46, 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 1232 8.00 N 1189 7.00 C 5067 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 292.7 milliseconds 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1714 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 91.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'a' and resid 31 through 53 removed outlier: 4.008A pdb=" N THR a 38 " --> pdb=" O ALA a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 109 removed outlier: 4.405A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL a 108 " --> pdb=" O ASN a 104 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU a 109 " --> pdb=" O TRP a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 154 removed outlier: 3.893A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 157 through 165 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 removed outlier: 3.703A pdb=" N ILE a 175 " --> pdb=" O ALA a 171 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL a 176 " --> pdb=" O PRO a 172 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 3.584A pdb=" N ARG a 188 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA a 201 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 246 removed outlier: 4.606A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.950A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 49 Processing helix chain 'b' and resid 49 through 64 Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 39 Processing helix chain '1' and resid 6 through 46 removed outlier: 3.935A pdb=" N THR 1 10 " --> pdb=" O ASN 1 6 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA 1 13 " --> pdb=" O ILE 1 9 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY 1 18 " --> pdb=" O LEU 1 14 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY 1 23 " --> pdb=" O LEU 1 19 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY 1 33 " --> pdb=" O GLY 1 29 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA 1 38 " --> pdb=" O ILE 1 34 " (cutoff:3.500A) Processing helix chain '1' and resid 47 through 52 removed outlier: 4.383A pdb=" N GLY 1 51 " --> pdb=" O GLU 1 48 " (cutoff:3.500A) Processing helix chain '1' and resid 53 through 80 Processing helix chain '2' and resid 6 through 46 Processing helix chain '2' and resid 49 through 82 removed outlier: 3.737A pdb=" N PHE 2 54 " --> pdb=" O GLN 2 50 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR 2 55 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) Proline residue: 2 56 - end of helix removed outlier: 3.600A pdb=" N LEU 2 63 " --> pdb=" O ILE 2 59 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA 2 67 " --> pdb=" O LEU 2 63 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE 2 70 " --> pdb=" O ALA 2 66 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 46 Processing helix chain '3' and resid 49 through 80 removed outlier: 3.675A pdb=" N PHE 3 54 " --> pdb=" O GLN 3 50 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N THR 3 55 " --> pdb=" O GLY 3 51 " (cutoff:3.500A) Proline residue: 3 56 - end of helix removed outlier: 4.242A pdb=" N ALA 3 67 " --> pdb=" O LEU 3 63 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR 3 68 " --> pdb=" O VAL 3 64 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE 3 70 " --> pdb=" O ALA 3 66 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU 3 77 " --> pdb=" O ALA 3 73 " (cutoff:3.500A) Processing helix chain '4' and resid 6 through 46 Processing helix chain '4' and resid 49 through 81 removed outlier: 4.214A 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 removed outlier: 3.633A pdb=" N ALA 5 38 " --> pdb=" O ILE 5 34 " (cutoff:3.500A) Processing helix chain '5' and resid 49 through 81 removed outlier: 5.140A 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 81 removed outlier: 3.566A pdb=" N PHE 6 54 " --> pdb=" O GLN 6 50 " (cutoff:3.500A) removed outlier: 4.504A 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 49 through 80 removed outlier: 4.292A 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 45 Processing helix chain '8' and resid 46 through 48 No H-bonds generated for 'chain '8' and resid 46 through 48' Processing helix chain '8' and resid 49 through 81 removed outlier: 3.636A pdb=" N LEU 8 53 " --> pdb=" O ALA 8 49 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR 8 55 " --> pdb=" O GLY 8 51 " (cutoff:3.500A) Proline residue: 8 56 - end of helix removed outlier: 3.852A pdb=" N ILE 8 70 " --> pdb=" O ALA 8 66 " (cutoff:3.500A) Processing helix chain '9' and resid 6 through 46 removed outlier: 3.813A pdb=" N ARG 9 45 " --> pdb=" O SER 9 41 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN 9 46 " --> pdb=" O GLY 9 42 " (cutoff:3.500A) Processing helix chain '9' and resid 49 through 80 removed outlier: 4.319A pdb=" N THR 9 55 " --> pdb=" O GLY 9 51 " (cutoff:3.500A) Proline residue: 9 56 - end of helix removed outlier: 3.586A pdb=" N TYR 9 68 " --> pdb=" O VAL 9 64 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE 9 70 " --> pdb=" O ALA 9 66 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 2169 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: 1.25 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 2326 1.36 - 1.51: 2614 1.51 - 1.65: 2711 1.65 - 1.80: 41 1.80 - 1.94: 17 Bond restraints: 7709 Sorted by residual: bond pdb=" C07 BQ1 5 601 " pdb=" C10 BQ1 5 601 " ideal model delta sigma weight residual 1.510 1.605 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C07 BQ1 1 601 " pdb=" C10 BQ1 1 601 " ideal model delta sigma weight residual 1.510 1.604 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C07 BQ1 9 601 " pdb=" C10 BQ1 9 601 " ideal model delta sigma weight residual 1.510 1.603 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" C17 BQ1 7 601 " pdb=" O03 BQ1 7 601 " ideal model delta sigma weight residual 1.330 1.423 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C07 BQ1 8 601 " pdb=" C10 BQ1 8 601 " ideal model delta sigma weight residual 1.510 1.603 -0.093 2.00e-02 2.50e+03 2.14e+01 ... (remaining 7704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 9986 1.62 - 3.24: 412 3.24 - 4.85: 82 4.85 - 6.47: 18 6.47 - 8.09: 2 Bond angle restraints: 10500 Sorted by residual: angle pdb=" C VAL b 50 " pdb=" CA VAL b 50 " pdb=" CB VAL b 50 " ideal model delta sigma weight residual 114.00 110.34 3.66 1.31e+00 5.83e-01 7.82e+00 angle pdb=" C08 BQ1 7 601 " pdb=" C11 BQ1 7 601 " pdb=" N04 BQ1 7 601 " ideal model delta sigma weight residual 112.02 103.93 8.09 3.00e+00 1.11e-01 7.27e+00 angle pdb=" C17 BQ1 1 601 " pdb=" O03 BQ1 1 601 " pdb=" C37 BQ1 1 601 " ideal model delta sigma weight residual 118.29 110.74 7.55 3.00e+00 1.11e-01 6.33e+00 angle pdb=" N PRO 9 83 " pdb=" CA PRO 9 83 " pdb=" C PRO 9 83 " ideal model delta sigma weight residual 111.03 114.86 -3.83 1.54e+00 4.22e-01 6.18e+00 angle pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " pdb=" CG TYR a 145 " ideal model delta sigma weight residual 113.90 117.98 -4.08 1.80e+00 3.09e-01 5.14e+00 ... (remaining 10495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.17: 3958 19.17 - 38.35: 286 38.35 - 57.52: 73 57.52 - 76.70: 24 76.70 - 95.87: 20 Dihedral angle restraints: 4361 sinusoidal: 1628 harmonic: 2733 Sorted by residual: dihedral pdb=" CA PHE a 206 " pdb=" C PHE a 206 " pdb=" N PRO a 207 " pdb=" CA PRO a 207 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA LYS a 52 " pdb=" C LYS a 52 " pdb=" N VAL a 53 " pdb=" CA VAL a 53 " ideal model delta harmonic sigma weight residual -180.00 -158.63 -21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ALA 8 49 " pdb=" C ALA 8 49 " pdb=" N GLN 8 50 " pdb=" CA GLN 8 50 " ideal model delta harmonic sigma weight residual -180.00 -162.05 -17.95 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 4358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1141 0.086 - 0.172: 65 0.172 - 0.258: 1 0.258 - 0.344: 3 0.344 - 0.430: 4 Chirality restraints: 1214 Sorted by residual: chirality pdb=" C07 BQ1 6 601 " pdb=" C06 BQ1 6 601 " pdb=" C10 BQ1 6 601 " pdb=" C12 BQ1 6 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.83 0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" C07 BQ1 4 601 " pdb=" C06 BQ1 4 601 " pdb=" C10 BQ1 4 601 " pdb=" C12 BQ1 4 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.82 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" C07 BQ1 1 601 " pdb=" C06 BQ1 1 601 " pdb=" C10 BQ1 1 601 " pdb=" C12 BQ1 1 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.77 0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 1211 not shown) Planarity restraints: 1295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE a 99 " -0.016 2.00e-02 2.50e+03 1.40e-02 3.41e+00 pdb=" CG PHE a 99 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE a 99 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE a 99 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE a 99 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE a 99 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE a 99 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL b 50 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO b 51 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO b 51 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO b 51 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE a 190 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C PHE a 190 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE a 190 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY a 191 " 0.010 2.00e-02 2.50e+03 ... (remaining 1292 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 21 2.48 - 3.09: 6308 3.09 - 3.69: 11803 3.69 - 4.30: 17587 4.30 - 4.90: 29211 Nonbonded interactions: 64930 Sorted by model distance: nonbonded pdb=" OH TYR 7 68 " pdb=" OD1 ASN 8 71 " model vdw 1.879 3.040 nonbonded pdb=" O ALA a 216 " pdb=" OG1 THR a 220 " model vdw 2.169 3.040 nonbonded pdb=" OH TYR 1 68 " pdb=" OD1 ASN 2 71 " model vdw 2.178 3.040 nonbonded pdb=" OE1 GLU 4 65 " pdb=" N04 BQ1 4 601 " model vdw 2.209 3.120 nonbonded pdb=" OE2 GLU 8 65 " pdb=" N04 BQ1 8 601 " model vdw 2.222 3.120 ... (remaining 64925 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 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 '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 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 '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 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 47 or (resid 48 through 49 and (name N or name C \ A or name C or name O or name CB )) or resid 50 through 51 or (resid 52 and (nam \ e 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 47 or (resid 48 through 49 and (name N or name C \ A or name C or name O or name CB )) or resid 50 through 85)) selection = (chain '8' 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 '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: 2.890 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.100 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 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 : 0.017 0.846 7711 Z= 1.376 Angle : 0.792 8.091 10500 Z= 0.420 Chirality : 0.053 0.430 1214 Planarity : 0.006 0.046 1295 Dihedral : 16.800 95.870 2647 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.15 % Allowed : 6.20 % Favored : 93.65 % 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 are not related in a simple way. whole: -2.65 (0.22), residues: 991 helix: -1.36 (0.15), residues: 818 sheet: None (None), residues: 0 loop : -2.78 (0.42), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 188 TYR 0.019 0.002 TYR a 145 PHE 0.032 0.002 PHE a 99 TRP 0.010 0.002 TRP a 212 HIS 0.007 0.002 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.01064 ( 7709) covalent geometry : angle 0.79202 (10500) hydrogen bonds : bond 0.16804 ( 726) hydrogen bonds : angle 8.25268 ( 2169) Misc. bond : bond 0.79573 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 75 MET cc_start: 0.7036 (tmm) cc_final: 0.6802 (ttt) REVERT: 3 85 LEU cc_start: 0.7786 (tp) cc_final: 0.7563 (tt) REVERT: 6 85 LEU cc_start: 0.7441 (tp) cc_final: 0.7182 (tp) REVERT: 8 78 PHE cc_start: 0.6622 (m-10) cc_final: 0.6397 (m-80) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.0709 time to fit residues: 7.0388 Evaluate side-chains 62 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.152080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.139403 restraints weight = 9005.980| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.64 r_work: 0.3681 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 7711 Z= 0.222 Angle : 0.680 7.033 10500 Z= 0.347 Chirality : 0.043 0.142 1214 Planarity : 0.006 0.061 1295 Dihedral : 13.572 121.276 1234 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.59 % Allowed : 10.34 % Favored : 89.07 % 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 are not related in a simple way. whole: 1.33 (0.25), residues: 991 helix: 1.04 (0.17), residues: 838 sheet: None (None), residues: 0 loop : 0.51 (0.57), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 188 TYR 0.021 0.002 TYR a 145 PHE 0.025 0.002 PHE a 99 TRP 0.018 0.002 TRP a 212 HIS 0.006 0.002 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 7709) covalent geometry : angle 0.67998 (10500) hydrogen bonds : bond 0.05276 ( 726) hydrogen bonds : angle 5.00376 ( 2169) Misc. bond : bond 0.00350 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: a 73 MET cc_start: 0.7212 (mmp) cc_final: 0.6767 (mmp) REVERT: a 188 ARG cc_start: 0.8189 (ttm110) cc_final: 0.7979 (ttm110) REVERT: a 199 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7916 (tt) REVERT: a 235 LEU cc_start: 0.7839 (tp) cc_final: 0.7575 (tp) REVERT: d 38 ARG cc_start: 0.7267 (ttm110) cc_final: 0.7046 (ttp-170) REVERT: 1 10 THR cc_start: 0.8423 (m) cc_final: 0.8188 (t) REVERT: 2 75 MET cc_start: 0.6913 (tmm) cc_final: 0.6453 (ttt) REVERT: 3 85 LEU cc_start: 0.8192 (tp) cc_final: 0.7897 (tt) REVERT: 5 21 MET cc_start: 0.7692 (mmm) cc_final: 0.6889 (mtp) REVERT: 9 10 THR cc_start: 0.8090 (t) cc_final: 0.7747 (t) outliers start: 4 outliers final: 1 residues processed: 64 average time/residue: 0.0670 time to fit residues: 6.3005 Evaluate side-chains 64 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain a residue 199 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.150180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.137449 restraints weight = 8967.911| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.62 r_work: 0.3660 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 7711 Z= 0.222 Angle : 0.662 9.173 10500 Z= 0.336 Chirality : 0.042 0.140 1214 Planarity : 0.005 0.060 1295 Dihedral : 12.972 131.131 1234 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.03 % Allowed : 12.70 % Favored : 86.26 % 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 are not related in a simple way. whole: 2.30 (0.26), residues: 991 helix: 1.72 (0.17), residues: 833 sheet: None (None), residues: 0 loop : 0.78 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 9 52 TYR 0.021 0.002 TYR a 145 PHE 0.023 0.002 PHE a 99 TRP 0.016 0.002 TRP a 212 HIS 0.005 0.002 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 7709) covalent geometry : angle 0.66223 (10500) hydrogen bonds : bond 0.04901 ( 726) hydrogen bonds : angle 4.70970 ( 2169) Misc. bond : bond 0.00249 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 73 MET cc_start: 0.7442 (mmp) cc_final: 0.6983 (mmp) REVERT: a 199 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7992 (tt) REVERT: a 231 PHE cc_start: 0.7477 (t80) cc_final: 0.7196 (t80) REVERT: d 38 ARG cc_start: 0.7252 (ttm110) cc_final: 0.7046 (ttp-170) REVERT: 3 21 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6977 (mpp) REVERT: 3 85 LEU cc_start: 0.8106 (tp) cc_final: 0.7831 (tt) REVERT: 4 75 MET cc_start: 0.7943 (tmm) cc_final: 0.7593 (tmm) REVERT: 9 10 THR cc_start: 0.8043 (t) cc_final: 0.7801 (t) outliers start: 7 outliers final: 2 residues processed: 69 average time/residue: 0.0670 time to fit residues: 7.0161 Evaluate side-chains 71 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain 3 residue 21 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 63 optimal weight: 0.0980 chunk 92 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 215 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.150494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.137735 restraints weight = 9063.556| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.63 r_work: 0.3664 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 7711 Z= 0.193 Angle : 0.615 6.982 10500 Z= 0.310 Chirality : 0.041 0.132 1214 Planarity : 0.005 0.060 1295 Dihedral : 12.496 133.529 1234 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.22 % Allowed : 13.44 % Favored : 84.34 % 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 are not related in a simple way. whole: 2.75 (0.26), residues: 991 helix: 2.02 (0.17), residues: 831 sheet: None (None), residues: 0 loop : 0.98 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 9 52 TYR 0.021 0.001 TYR a 145 PHE 0.019 0.002 PHE a 99 TRP 0.014 0.002 TRP a 212 HIS 0.005 0.002 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 7709) covalent geometry : angle 0.61480 (10500) hydrogen bonds : bond 0.04639 ( 726) hydrogen bonds : angle 4.58643 ( 2169) Misc. bond : bond 0.00207 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.240 Fit side-chains REVERT: a 62 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7653 (t) REVERT: a 73 MET cc_start: 0.7458 (mmp) cc_final: 0.7003 (mmp) REVERT: a 231 PHE cc_start: 0.7481 (t80) cc_final: 0.7246 (t80) REVERT: d 38 ARG cc_start: 0.7340 (ttm110) cc_final: 0.7133 (ttp-170) REVERT: 1 50 GLN cc_start: 0.7471 (pt0) cc_final: 0.7148 (pt0) REVERT: 2 21 MET cc_start: 0.7188 (tpt) cc_final: 0.6971 (tpt) REVERT: 2 75 MET cc_start: 0.6840 (tmm) cc_final: 0.6370 (ttp) REVERT: 4 75 MET cc_start: 0.7961 (tmm) cc_final: 0.7572 (tmm) REVERT: 7 21 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.5878 (mpp) REVERT: 8 47 PRO cc_start: 0.8006 (Cg_endo) cc_final: 0.7759 (Cg_exo) REVERT: 9 10 THR cc_start: 0.8030 (t) cc_final: 0.7802 (t) outliers start: 15 outliers final: 5 residues processed: 77 average time/residue: 0.0742 time to fit residues: 8.3811 Evaluate side-chains 74 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain d residue 3 ILE Chi-restraints excluded: chain 4 residue 85 LEU Chi-restraints excluded: chain 7 residue 21 MET Chi-restraints excluded: chain 9 residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 20 optimal weight: 0.0370 chunk 15 optimal weight: 0.3980 chunk 88 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.153572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.142281 restraints weight = 8675.104| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.46 r_work: 0.3685 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7711 Z= 0.184 Angle : 0.620 9.253 10500 Z= 0.308 Chirality : 0.041 0.143 1214 Planarity : 0.004 0.059 1295 Dihedral : 12.125 133.996 1234 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.92 % Allowed : 14.62 % Favored : 83.46 % 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 are not related in a simple way. whole: 2.89 (0.25), residues: 991 helix: 2.14 (0.17), residues: 831 sheet: None (None), residues: 0 loop : 0.87 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 9 52 TYR 0.021 0.001 TYR a 145 PHE 0.017 0.001 PHE a 99 TRP 0.014 0.002 TRP a 212 HIS 0.004 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 7709) covalent geometry : angle 0.62049 (10500) hydrogen bonds : bond 0.04553 ( 726) hydrogen bonds : angle 4.53514 ( 2169) Misc. bond : bond 0.00200 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: a 62 VAL cc_start: 0.7948 (OUTLIER) cc_final: 0.7626 (t) REVERT: a 73 MET cc_start: 0.7250 (mmp) cc_final: 0.6777 (mmp) REVERT: a 231 PHE cc_start: 0.7398 (t80) cc_final: 0.7169 (t80) REVERT: 1 50 GLN cc_start: 0.7408 (pt0) cc_final: 0.7171 (pt0) REVERT: 4 75 MET cc_start: 0.7964 (tmm) cc_final: 0.7539 (tmm) REVERT: 8 47 PRO cc_start: 0.7859 (Cg_endo) cc_final: 0.7654 (Cg_exo) outliers start: 13 outliers final: 4 residues processed: 75 average time/residue: 0.0664 time to fit residues: 7.6381 Evaluate side-chains 71 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain d residue 3 ILE Chi-restraints excluded: chain d residue 19 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 52 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 67 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 73 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.151726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.140161 restraints weight = 8738.926| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.50 r_work: 0.3685 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7711 Z= 0.172 Angle : 0.616 8.086 10500 Z= 0.303 Chirality : 0.041 0.137 1214 Planarity : 0.004 0.059 1295 Dihedral : 11.727 133.879 1234 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.03 % Allowed : 16.99 % Favored : 81.98 % 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 are not related in a simple way. whole: 2.99 (0.26), residues: 991 helix: 2.22 (0.17), residues: 836 sheet: None (None), residues: 0 loop : 0.75 (0.54), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 9 52 TYR 0.020 0.001 TYR a 145 PHE 0.018 0.001 PHE 9 74 TRP 0.014 0.002 TRP a 212 HIS 0.004 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7709) covalent geometry : angle 0.61567 (10500) hydrogen bonds : bond 0.04404 ( 726) hydrogen bonds : angle 4.46403 ( 2169) Misc. bond : bond 0.00186 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.257 Fit side-chains REVERT: a 62 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7609 (t) REVERT: a 73 MET cc_start: 0.7285 (mmp) cc_final: 0.6792 (mmp) REVERT: a 231 PHE cc_start: 0.7408 (t80) cc_final: 0.7167 (t80) REVERT: 1 10 THR cc_start: 0.8628 (m) cc_final: 0.8312 (t) REVERT: 1 50 GLN cc_start: 0.7423 (pt0) cc_final: 0.7177 (pt0) REVERT: 1 78 PHE cc_start: 0.6459 (m-10) cc_final: 0.6178 (m-10) REVERT: 4 75 MET cc_start: 0.7944 (tmm) cc_final: 0.7542 (tmm) REVERT: 6 21 MET cc_start: 0.7159 (mtp) cc_final: 0.6942 (mtp) outliers start: 7 outliers final: 4 residues processed: 72 average time/residue: 0.0662 time to fit residues: 7.2345 Evaluate side-chains 71 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain 7 residue 72 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 0.0010 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.151561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.140054 restraints weight = 8775.780| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.50 r_work: 0.3662 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7711 Z= 0.176 Angle : 0.623 7.677 10500 Z= 0.305 Chirality : 0.041 0.136 1214 Planarity : 0.004 0.059 1295 Dihedral : 11.513 134.666 1234 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.89 % Allowed : 17.58 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.25), residues: 991 helix: 2.27 (0.17), residues: 835 sheet: None (None), residues: 0 loop : 0.60 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 9 52 TYR 0.019 0.001 TYR a 145 PHE 0.019 0.001 PHE 9 74 TRP 0.014 0.002 TRP a 212 HIS 0.004 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 7709) covalent geometry : angle 0.62286 (10500) hydrogen bonds : bond 0.04382 ( 726) hydrogen bonds : angle 4.46034 ( 2169) Misc. bond : bond 0.00189 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.218 Fit side-chains REVERT: a 73 MET cc_start: 0.7314 (mmp) cc_final: 0.6850 (mmp) REVERT: a 190 PHE cc_start: 0.7517 (t80) cc_final: 0.7204 (t80) REVERT: a 231 PHE cc_start: 0.7427 (t80) cc_final: 0.7213 (t80) REVERT: d 30 MET cc_start: 0.6874 (tpp) cc_final: 0.6403 (tpp) REVERT: 1 50 GLN cc_start: 0.7399 (pt0) cc_final: 0.7131 (pt0) REVERT: 1 78 PHE cc_start: 0.6424 (m-10) cc_final: 0.6124 (m-10) REVERT: 4 75 MET cc_start: 0.7939 (tmm) cc_final: 0.7510 (tmm) REVERT: 8 75 MET cc_start: 0.6885 (tmm) cc_final: 0.6018 (tmm) outliers start: 6 outliers final: 4 residues processed: 69 average time/residue: 0.0675 time to fit residues: 7.0644 Evaluate side-chains 70 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain d residue 3 ILE Chi-restraints excluded: chain d residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.0370 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 0.0980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.153566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.142097 restraints weight = 8763.237| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.49 r_work: 0.3680 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7711 Z= 0.180 Angle : 0.619 9.145 10500 Z= 0.304 Chirality : 0.041 0.138 1214 Planarity : 0.004 0.059 1295 Dihedral : 11.316 135.888 1234 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.74 % Allowed : 19.65 % Favored : 79.62 % 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 are not related in a simple way. whole: 3.01 (0.25), residues: 991 helix: 2.27 (0.17), residues: 836 sheet: None (None), residues: 0 loop : 0.52 (0.54), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 9 52 TYR 0.019 0.001 TYR a 145 PHE 0.015 0.001 PHE 5 74 TRP 0.015 0.002 TRP a 212 HIS 0.004 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 7709) covalent geometry : angle 0.61939 (10500) hydrogen bonds : bond 0.04383 ( 726) hydrogen bonds : angle 4.44687 ( 2169) Misc. bond : bond 0.00182 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.220 Fit side-chains REVERT: a 231 PHE cc_start: 0.7419 (t80) cc_final: 0.7212 (t80) REVERT: d 30 MET cc_start: 0.6886 (tpp) cc_final: 0.6392 (tpp) REVERT: 1 50 GLN cc_start: 0.7394 (pt0) cc_final: 0.7120 (pt0) REVERT: 4 75 MET cc_start: 0.7941 (tmm) cc_final: 0.7530 (tmm) REVERT: 8 75 MET cc_start: 0.6448 (tmm) cc_final: 0.5843 (tmm) REVERT: 9 21 MET cc_start: 0.7762 (mmm) cc_final: 0.7366 (mmm) outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 0.0722 time to fit residues: 7.4516 Evaluate side-chains 67 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain d residue 3 ILE Chi-restraints excluded: chain d residue 19 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 chunk 63 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.154090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.142644 restraints weight = 8655.063| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.47 r_work: 0.3689 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7711 Z= 0.163 Angle : 0.603 9.547 10500 Z= 0.297 Chirality : 0.041 0.140 1214 Planarity : 0.004 0.059 1295 Dihedral : 11.084 136.409 1234 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.33 % Allowed : 18.91 % Favored : 79.76 % 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 are not related in a simple way. whole: 3.13 (0.25), residues: 991 helix: 2.37 (0.17), residues: 837 sheet: None (None), residues: 0 loop : 0.48 (0.53), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 9 52 TYR 0.020 0.001 TYR a 145 PHE 0.029 0.001 PHE a 190 TRP 0.015 0.002 TRP a 212 HIS 0.004 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7709) covalent geometry : angle 0.60319 (10500) hydrogen bonds : bond 0.04254 ( 726) hydrogen bonds : angle 4.39470 ( 2169) Misc. bond : bond 0.00155 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.252 Fit side-chains REVERT: a 62 VAL cc_start: 0.7845 (OUTLIER) cc_final: 0.7534 (t) REVERT: d 30 MET cc_start: 0.6871 (tpp) cc_final: 0.6389 (tpp) REVERT: 4 54 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.6683 (m-10) REVERT: 4 75 MET cc_start: 0.7928 (tmm) cc_final: 0.7512 (tmm) REVERT: 5 21 MET cc_start: 0.7529 (mmm) cc_final: 0.6891 (mtp) REVERT: 9 21 MET cc_start: 0.7730 (mmm) cc_final: 0.7336 (mpp) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.0699 time to fit residues: 7.5417 Evaluate side-chains 70 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain d residue 3 ILE Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 8 residue 72 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.151207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.139810 restraints weight = 8663.352| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.46 r_work: 0.3653 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7711 Z= 0.227 Angle : 0.652 10.171 10500 Z= 0.325 Chirality : 0.043 0.149 1214 Planarity : 0.005 0.059 1295 Dihedral : 11.261 138.872 1234 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.03 % Allowed : 19.50 % Favored : 79.47 % 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 are not related in a simple way. whole: 2.84 (0.25), residues: 991 helix: 2.15 (0.17), residues: 837 sheet: None (None), residues: 0 loop : 0.47 (0.54), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 9 52 TYR 0.019 0.001 TYR a 145 PHE 0.026 0.002 PHE a 190 TRP 0.016 0.002 TRP a 212 HIS 0.004 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 7709) covalent geometry : angle 0.65223 (10500) hydrogen bonds : bond 0.04622 ( 726) hydrogen bonds : angle 4.53403 ( 2169) Misc. bond : bond 0.00210 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: a 62 VAL cc_start: 0.7928 (OUTLIER) cc_final: 0.7630 (t) REVERT: d 30 MET cc_start: 0.6906 (tpp) cc_final: 0.6415 (tpp) REVERT: 2 75 MET cc_start: 0.6966 (ttp) cc_final: 0.6661 (ttp) REVERT: 4 75 MET cc_start: 0.7892 (tmm) cc_final: 0.7495 (tmm) REVERT: 5 21 MET cc_start: 0.7531 (mmm) cc_final: 0.6877 (mtp) REVERT: 9 21 MET cc_start: 0.7765 (mmm) cc_final: 0.7550 (tpp) outliers start: 7 outliers final: 5 residues processed: 69 average time/residue: 0.0713 time to fit residues: 7.4506 Evaluate side-chains 70 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain a residue 192 ASN Chi-restraints excluded: chain d residue 3 ILE Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain 4 residue 77 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 63 optimal weight: 0.1980 chunk 72 optimal weight: 0.0870 chunk 44 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.153496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.142158 restraints weight = 8577.142| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.46 r_work: 0.3682 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7711 Z= 0.170 Angle : 0.616 10.134 10500 Z= 0.304 Chirality : 0.041 0.144 1214 Planarity : 0.004 0.058 1295 Dihedral : 11.053 140.224 1234 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.33 % Allowed : 19.35 % Favored : 79.32 % 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 are not related in a simple way. whole: 3.02 (0.25), residues: 991 helix: 2.30 (0.17), residues: 837 sheet: None (None), residues: 0 loop : 0.35 (0.53), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 9 52 TYR 0.020 0.001 TYR a 145 PHE 0.026 0.001 PHE a 190 TRP 0.018 0.002 TRP a 212 HIS 0.004 0.001 HIS a 158 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7709) covalent geometry : angle 0.61574 (10500) hydrogen bonds : bond 0.04338 ( 726) hydrogen bonds : angle 4.43744 ( 2169) Misc. bond : bond 0.00146 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1648.42 seconds wall clock time: 28 minutes 59.54 seconds (1739.54 seconds total)