Starting phenix.real_space_refine on Wed Feb 12 07:15:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jgc_22321/02_2025/7jgc_22321.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jgc_22321/02_2025/7jgc_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_22321/02_2025/7jgc_22321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jgc_22321/02_2025/7jgc_22321.map" model { file = "/net/cci-nas-00/data/ceres_data/7jgc_22321/02_2025/7jgc_22321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jgc_22321/02_2025/7jgc_22321.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLU:plan': 2, 'ASN:plan1': 1} 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: 5.50, per 1000 atoms: 0.73 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: 2.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.64 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: 2.41 Time building geometry restraints manager: 2.43 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: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.250 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.240 ------------------------------------------------------------------------------- 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 : 0.011 0.113 7709 Z= 0.690 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (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 TRP 0.010 0.002 TRP a 212 HIS 0.007 0.002 HIS a 158 PHE 0.032 0.002 PHE a 99 TYR 0.019 0.002 TYR a 145 ARG 0.007 0.001 ARG a 188 *********************** 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 : 0.707 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: 0.6396 (m-80) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.1803 time to fit residues: 17.6389 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 : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.4980 chunk 75 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.152600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.139942 restraints weight = 8953.003| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.64 r_work: 0.3692 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 7709 Z= 0.304 Angle : 0.674 7.037 10500 Z= 0.343 Chirality : 0.043 0.140 1214 Planarity : 0.005 0.060 1295 Dihedral : 13.450 122.112 1234 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.74 % Allowed : 10.34 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.26), residues: 991 helix: 1.16 (0.17), residues: 833 sheet: None (None), residues: 0 loop : 0.61 (0.56), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a 212 HIS 0.006 0.002 HIS a 158 PHE 0.025 0.002 PHE a 99 TYR 0.021 0.002 TYR a 145 ARG 0.005 0.001 ARG a 188 *********************** 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 68 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: a 73 MET cc_start: 0.7222 (mmp) cc_final: 0.6790 (mmp) REVERT: a 83 MET cc_start: 0.6263 (OUTLIER) cc_final: 0.5895 (tpp) REVERT: a 188 ARG cc_start: 0.8167 (ttm110) cc_final: 0.7948 (ttm110) REVERT: a 199 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7913 (tt) REVERT: a 235 LEU cc_start: 0.7853 (tp) cc_final: 0.7594 (tp) REVERT: d 38 ARG cc_start: 0.7240 (ttm110) cc_final: 0.7013 (ttp-170) REVERT: 1 10 THR cc_start: 0.8370 (m) cc_final: 0.8147 (t) REVERT: 2 75 MET cc_start: 0.6903 (tmm) cc_final: 0.6425 (ttt) REVERT: 3 85 LEU cc_start: 0.8203 (tp) cc_final: 0.7910 (tt) REVERT: 5 21 MET cc_start: 0.7687 (mmm) cc_final: 0.6869 (mtp) REVERT: 9 10 THR cc_start: 0.8085 (t) cc_final: 0.7768 (t) outliers start: 5 outliers final: 0 residues processed: 66 average time/residue: 0.1786 time to fit residues: 17.2084 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 : 0.693 ------------------------------------------------------------------------------- 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: 1.9990 chunk 65 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 67 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.151208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.138477 restraints weight = 8932.837| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.63 r_work: 0.3674 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 7709 Z= 0.291 Angle : 0.654 9.684 10500 Z= 0.328 Chirality : 0.042 0.136 1214 Planarity : 0.005 0.061 1295 Dihedral : 12.892 129.416 1234 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.03 % Allowed : 12.56 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.26), residues: 991 helix: 1.78 (0.17), residues: 833 sheet: None (None), residues: 0 loop : 0.87 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP a 212 HIS 0.005 0.002 HIS a 158 PHE 0.022 0.002 PHE a 99 TYR 0.021 0.002 TYR a 145 ARG 0.003 0.000 ARG 9 52 *********************** 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 73 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: a 73 MET cc_start: 0.7412 (mmp) cc_final: 0.6961 (mmp) REVERT: a 199 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7972 (tt) REVERT: a 231 PHE cc_start: 0.7445 (t80) cc_final: 0.7174 (t80) REVERT: d 38 ARG cc_start: 0.7200 (ttm110) cc_final: 0.6983 (ttp-170) REVERT: 3 85 LEU cc_start: 0.8135 (tp) cc_final: 0.7866 (tt) REVERT: 4 75 MET cc_start: 0.7900 (tmm) cc_final: 0.7524 (tmm) REVERT: 9 10 THR cc_start: 0.8032 (t) cc_final: 0.7779 (t) REVERT: 9 21 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.6909 (mpp) outliers start: 7 outliers final: 3 residues processed: 70 average time/residue: 0.1858 time to fit residues: 19.6980 Evaluate side-chains 72 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 7 residue 72 LEU Chi-restraints excluded: chain 9 residue 21 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 0.0980 chunk 95 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.150212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137538 restraints weight = 8916.755| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.62 r_work: 0.3655 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 7709 Z= 0.287 Angle : 0.631 7.084 10500 Z= 0.316 Chirality : 0.041 0.136 1214 Planarity : 0.005 0.060 1295 Dihedral : 12.507 132.967 1234 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.07 % Allowed : 13.15 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.26), residues: 991 helix: 2.00 (0.17), residues: 831 sheet: None (None), residues: 0 loop : 0.98 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP a 212 HIS 0.005 0.002 HIS a 158 PHE 0.020 0.002 PHE a 99 TYR 0.021 0.001 TYR a 145 ARG 0.003 0.000 ARG 9 52 *********************** 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 81 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 62 VAL cc_start: 0.7957 (OUTLIER) cc_final: 0.7647 (t) REVERT: a 73 MET cc_start: 0.7443 (mmp) cc_final: 0.6979 (mmp) REVERT: a 199 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7955 (tt) REVERT: a 231 PHE cc_start: 0.7479 (t80) cc_final: 0.7250 (t80) REVERT: d 38 ARG cc_start: 0.7326 (ttm110) cc_final: 0.7124 (ttp-170) REVERT: 1 50 GLN cc_start: 0.7479 (pt0) cc_final: 0.7157 (pt0) REVERT: 3 21 MET cc_start: 0.7691 (mmm) cc_final: 0.7347 (tpp) REVERT: 4 75 MET cc_start: 0.7938 (tmm) cc_final: 0.7563 (tmm) REVERT: 7 21 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.6639 (mpp) REVERT: 9 10 THR cc_start: 0.8034 (t) cc_final: 0.7802 (t) REVERT: 9 79 VAL cc_start: 0.8081 (m) cc_final: 0.7853 (t) outliers start: 14 outliers final: 5 residues processed: 77 average time/residue: 0.1776 time to fit residues: 19.7883 Evaluate side-chains 74 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 a residue 199 LEU Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain 4 residue 85 LEU Chi-restraints excluded: chain 7 residue 21 MET Chi-restraints excluded: chain 7 residue 72 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 4 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.153118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.141889 restraints weight = 8556.555| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.44 r_work: 0.3679 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7709 Z= 0.277 Angle : 0.621 9.041 10500 Z= 0.310 Chirality : 0.041 0.153 1214 Planarity : 0.005 0.060 1295 Dihedral : 12.095 134.222 1234 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.22 % Allowed : 14.77 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.25), residues: 991 helix: 2.12 (0.17), residues: 831 sheet: None (None), residues: 0 loop : 0.88 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP a 212 HIS 0.004 0.001 HIS a 158 PHE 0.017 0.001 PHE a 99 TYR 0.021 0.001 TYR a 145 ARG 0.003 0.000 ARG 9 52 *********************** 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 81 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: a 62 VAL cc_start: 0.7900 (OUTLIER) cc_final: 0.7581 (t) REVERT: a 73 MET cc_start: 0.7224 (mmp) cc_final: 0.6754 (mmp) REVERT: a 231 PHE cc_start: 0.7404 (t80) cc_final: 0.7183 (t80) REVERT: 1 50 GLN cc_start: 0.7406 (pt0) cc_final: 0.7018 (pt0) REVERT: 1 78 PHE cc_start: 0.6630 (m-10) cc_final: 0.6327 (m-10) REVERT: 2 75 MET cc_start: 0.6999 (tmm) cc_final: 0.6514 (ttp) REVERT: 3 21 MET cc_start: 0.7612 (mmm) cc_final: 0.7342 (tpp) REVERT: 4 75 MET cc_start: 0.7928 (tmm) cc_final: 0.7720 (tmm) REVERT: 7 21 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6682 (mpp) REVERT: 8 47 PRO cc_start: 0.7881 (Cg_endo) cc_final: 0.7669 (Cg_exo) REVERT: 9 10 THR cc_start: 0.8185 (t) cc_final: 0.7968 (t) outliers start: 15 outliers final: 7 residues processed: 74 average time/residue: 0.1512 time to fit residues: 16.7983 Evaluate side-chains 75 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 85 LEU Chi-restraints excluded: chain 7 residue 21 MET Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 8 residue 21 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 73 optimal weight: 0.4980 chunk 80 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.152309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.140782 restraints weight = 8620.930| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.46 r_work: 0.3663 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7709 Z= 0.290 Angle : 0.624 7.590 10500 Z= 0.310 Chirality : 0.042 0.147 1214 Planarity : 0.005 0.061 1295 Dihedral : 11.851 134.787 1234 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.33 % Allowed : 16.10 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.25), residues: 991 helix: 2.11 (0.17), residues: 835 sheet: None (None), residues: 0 loop : 0.60 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP a 212 HIS 0.004 0.002 HIS a 158 PHE 0.020 0.001 PHE 9 74 TYR 0.019 0.001 TYR a 145 ARG 0.003 0.000 ARG 9 52 *********************** 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 76 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 62 VAL cc_start: 0.7926 (OUTLIER) cc_final: 0.7642 (t) REVERT: a 73 MET cc_start: 0.7252 (mmp) cc_final: 0.6778 (mmp) REVERT: a 231 PHE cc_start: 0.7421 (t80) cc_final: 0.7183 (t80) REVERT: 1 50 GLN cc_start: 0.7404 (pt0) cc_final: 0.7148 (pt0) REVERT: 2 75 MET cc_start: 0.7020 (tmm) cc_final: 0.6732 (ttp) REVERT: 3 21 MET cc_start: 0.7573 (mmm) cc_final: 0.7328 (tpp) REVERT: 7 21 MET cc_start: 0.7063 (mpp) cc_final: 0.6690 (mpp) REVERT: 8 47 PRO cc_start: 0.7906 (Cg_endo) cc_final: 0.7699 (Cg_exo) REVERT: 9 10 THR cc_start: 0.8215 (t) cc_final: 0.8000 (t) REVERT: 9 21 MET cc_start: 0.7822 (mmm) cc_final: 0.7133 (mpp) outliers start: 9 outliers final: 7 residues processed: 72 average time/residue: 0.1565 time to fit residues: 17.0331 Evaluate side-chains 74 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 85 LEU Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 8 residue 21 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 66 optimal weight: 0.0370 chunk 33 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 84 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 overall best weight: 0.3058 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.154040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.141984 restraints weight = 8859.673| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.69 r_work: 0.3684 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7709 Z= 0.202 Angle : 0.581 8.196 10500 Z= 0.285 Chirality : 0.040 0.139 1214 Planarity : 0.004 0.061 1295 Dihedral : 11.228 132.184 1234 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.18 % Allowed : 17.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.25), residues: 991 helix: 2.43 (0.17), residues: 836 sheet: None (None), residues: 0 loop : 0.59 (0.54), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 212 HIS 0.004 0.001 HIS a 158 PHE 0.014 0.001 PHE 9 74 TYR 0.021 0.001 TYR a 145 ARG 0.002 0.000 ARG a 188 *********************** 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 74 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 73 MET cc_start: 0.7447 (mmp) cc_final: 0.6962 (mmp) REVERT: a 231 PHE cc_start: 0.7449 (t80) cc_final: 0.7245 (t80) REVERT: 1 10 THR cc_start: 0.8595 (m) cc_final: 0.8300 (t) REVERT: 1 50 GLN cc_start: 0.7384 (pt0) cc_final: 0.7103 (pt0) REVERT: 2 75 MET cc_start: 0.6990 (tmm) cc_final: 0.6699 (ttp) REVERT: 4 75 MET cc_start: 0.7927 (tmm) cc_final: 0.7640 (tmm) REVERT: 9 10 THR cc_start: 0.8118 (t) cc_final: 0.7899 (t) REVERT: 9 21 MET cc_start: 0.7763 (mmm) cc_final: 0.7360 (tpp) outliers start: 8 outliers final: 2 residues processed: 70 average time/residue: 0.1615 time to fit residues: 16.8561 Evaluate side-chains 67 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain 7 residue 72 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 73 optimal weight: 0.0670 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.154448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.142943 restraints weight = 8736.541| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.47 r_work: 0.3679 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7709 Z= 0.244 Angle : 0.610 8.179 10500 Z= 0.302 Chirality : 0.041 0.141 1214 Planarity : 0.005 0.060 1295 Dihedral : 11.110 130.662 1234 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.74 % Allowed : 18.91 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.26), residues: 991 helix: 2.39 (0.17), residues: 836 sheet: None (None), residues: 0 loop : 0.58 (0.54), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP a 212 HIS 0.004 0.001 HIS a 158 PHE 0.027 0.001 PHE a 190 TYR 0.020 0.001 TYR a 145 ARG 0.002 0.000 ARG 9 52 *********************** 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 : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 75 MET cc_start: 0.6946 (tmm) cc_final: 0.6670 (ttp) REVERT: 4 75 MET cc_start: 0.7960 (tmm) cc_final: 0.7608 (tmm) REVERT: 9 10 THR cc_start: 0.8144 (t) cc_final: 0.7930 (t) REVERT: 9 21 MET cc_start: 0.7777 (mmm) cc_final: 0.7407 (tpp) outliers start: 5 outliers final: 2 residues processed: 68 average time/residue: 0.1545 time to fit residues: 15.6808 Evaluate side-chains 68 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain d residue 3 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 56 optimal weight: 0.0170 chunk 82 optimal weight: 0.6980 chunk 99 optimal weight: 0.0870 chunk 95 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 84 optimal weight: 0.1980 chunk 75 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 overall best weight: 0.3196 ------------------------------------------------------------------------------- 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** 2 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.155118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.143543 restraints weight = 8721.563| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.49 r_work: 0.3699 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7709 Z= 0.206 Angle : 0.604 9.646 10500 Z= 0.293 Chirality : 0.040 0.177 1214 Planarity : 0.004 0.059 1295 Dihedral : 10.921 133.008 1234 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.44 % Allowed : 19.35 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.25), residues: 991 helix: 2.48 (0.17), residues: 837 sheet: None (None), residues: 0 loop : 0.61 (0.54), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 212 HIS 0.004 0.001 HIS a 158 PHE 0.024 0.001 PHE a 190 TYR 0.020 0.001 TYR a 145 ARG 0.002 0.000 ARG 9 52 *********************** 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 70 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 10 THR cc_start: 0.8644 (m) cc_final: 0.8352 (t) REVERT: 4 54 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.6709 (m-10) REVERT: 6 85 LEU cc_start: 0.7753 (mp) cc_final: 0.7494 (mp) REVERT: 9 10 THR cc_start: 0.8150 (t) cc_final: 0.7943 (t) REVERT: 9 21 MET cc_start: 0.7748 (mmm) cc_final: 0.7364 (tpp) outliers start: 3 outliers final: 2 residues processed: 68 average time/residue: 0.1556 time to fit residues: 15.9833 Evaluate side-chains 67 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain 2 residue 46 GLN Chi-restraints excluded: chain 4 residue 54 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 0.0870 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 88 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 40 optimal weight: 0.0770 chunk 98 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 overall best weight: 0.3316 ------------------------------------------------------------------------------- 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** 2 46 GLN ** 3 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.155137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.143659 restraints weight = 8738.570| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.49 r_work: 0.3700 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7709 Z= 0.209 Angle : 0.615 9.712 10500 Z= 0.298 Chirality : 0.040 0.183 1214 Planarity : 0.004 0.059 1295 Dihedral : 10.824 132.893 1234 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.59 % Allowed : 19.20 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.36 (0.25), residues: 991 helix: 2.53 (0.17), residues: 837 sheet: None (None), residues: 0 loop : 0.52 (0.53), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP a 212 HIS 0.004 0.001 HIS a 158 PHE 0.032 0.001 PHE a 190 TYR 0.020 0.001 TYR a 145 ARG 0.004 0.000 ARG 2 45 ********************** 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 70 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 10 THR cc_start: 0.8649 (m) cc_final: 0.8336 (t) REVERT: 4 54 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.6680 (m-10) REVERT: 6 85 LEU cc_start: 0.7808 (mp) cc_final: 0.7572 (mp) REVERT: 9 10 THR cc_start: 0.8143 (t) cc_final: 0.7941 (t) REVERT: 9 21 MET cc_start: 0.7780 (mmm) cc_final: 0.7385 (tpp) outliers start: 4 outliers final: 3 residues processed: 68 average time/residue: 0.1619 time to fit residues: 16.4070 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 : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain 2 residue 46 GLN Chi-restraints excluded: chain 4 residue 54 PHE 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 99 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.0870 chunk 88 optimal weight: 0.4980 chunk 65 optimal weight: 0.0570 chunk 82 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 90 optimal weight: 0.2980 overall best weight: 0.2076 ------------------------------------------------------------------------------- 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 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.155391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.143596 restraints weight = 8932.382| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.63 r_work: 0.3702 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7709 Z= 0.183 Angle : 0.598 10.255 10500 Z= 0.289 Chirality : 0.040 0.150 1214 Planarity : 0.004 0.059 1295 Dihedral : 10.636 132.485 1234 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.44 % Allowed : 19.65 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.50 (0.26), residues: 991 helix: 2.65 (0.17), residues: 837 sheet: None (None), residues: 0 loop : 0.40 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a 212 HIS 0.004 0.001 HIS a 158 PHE 0.032 0.001 PHE a 190 TYR 0.020 0.001 TYR a 145 ARG 0.002 0.000 ARG a 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3373.01 seconds wall clock time: 61 minutes 4.05 seconds (3664.05 seconds total)