Starting phenix.real_space_refine on Tue Feb 13 19:38:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgc_22321/02_2024/7jgc_22321.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgc_22321/02_2024/7jgc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgc_22321/02_2024/7jgc_22321.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgc_22321/02_2024/7jgc_22321.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgc_22321/02_2024/7jgc_22321.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgc_22321/02_2024/7jgc_22321.pdb" } 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 Residue "a ARG 50": "NH1" <-> "NH2" Residue "a GLU 67": "OE1" <-> "OE2" Residue "a ARG 188": "NH1" <-> "NH2" Residue "a TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 222": "OD1" <-> "OD2" Residue "b PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 59": "OE1" <-> "OE2" Residue "1 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 65": "OE1" <-> "OE2" Residue "2 ASP 32": "OD1" <-> "OD2" Residue "3 ASP 32": "OD1" <-> "OD2" Residue "3 GLU 65": "OE1" <-> "OE2" Residue "4 ARG 45": "NH1" <-> "NH2" Residue "5 GLU 65": "OE1" <-> "OE2" Residue "5 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 32": "OD1" <-> "OD2" Residue "6 GLU 65": "OE1" <-> "OE2" Residue "7 GLU 48": "OE1" <-> "OE2" Residue "7 PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 65": "OE1" <-> "OE2" Residue "9 ARG 45": "NH1" <-> "NH2" Residue "9 ARG 52": "NH1" <-> "NH2" Residue "9 TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.72, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 3.58 Conformation dependent library (CDL) restraints added in 1.5 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: 0.59 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: 2.26 Time building geometry restraints manager: 3.79 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: 97.37 - 104.74: 163 104.74 - 112.11: 3766 112.11 - 119.48: 2398 119.48 - 126.85: 4107 126.85 - 134.22: 66 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 2.440 nonbonded pdb=" O ALA a 216 " pdb=" OG1 THR a 220 " model vdw 2.169 2.440 nonbonded pdb=" OH TYR 1 68 " pdb=" OD1 ASN 2 71 " model vdw 2.178 2.440 nonbonded pdb=" OE1 GLU 4 65 " pdb=" N04 BQ1 4 601 " model vdw 2.209 2.520 nonbonded pdb=" OE2 GLU 8 65 " pdb=" N04 BQ1 8 601 " model vdw 2.222 2.520 ... (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 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: 1.820 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: 6.970 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.080 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.230 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.693 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: 0.1707 time to fit residues: 16.6761 Evaluate side-chains 62 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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: 0.5980 chunk 75 optimal weight: 0.4980 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** 1 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.1678 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= 0.293 Angle : 0.667 7.063 10500 Z= 0.338 Chirality : 0.043 0.137 1214 Planarity : 0.005 0.060 1295 Dihedral : 13.415 122.265 1234 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.16 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: 1.61 (0.26), residues: 991 helix: 1.26 (0.17), residues: 837 sheet: None (None), residues: 0 loop : 0.46 (0.57), 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 0.026 0.002 PHE a 99 TYR 0.021 0.002 TYR a 145 ARG 0.003 0.000 ARG 8 52 *********************** 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 fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 73 MET cc_start: 0.6160 (mmp) cc_final: 0.5830 (mmp) REVERT: a 199 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7858 (tt) REVERT: a 235 LEU cc_start: 0.7713 (tp) cc_final: 0.7437 (tp) REVERT: 3 85 LEU cc_start: 0.7883 (tp) cc_final: 0.7637 (tt) REVERT: 5 21 MET cc_start: 0.7151 (mmm) cc_final: 0.6610 (mtp) REVERT: 9 10 THR cc_start: 0.8015 (t) cc_final: 0.7731 (t) outliers start: 5 outliers final: 1 residues processed: 64 average time/residue: 0.1553 time to fit residues: 14.8750 Evaluate side-chains 62 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 98 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 89 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** 4 71 ASN 5 6 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 7709 Z= 0.283 Angle : 0.644 9.397 10500 Z= 0.322 Chirality : 0.041 0.134 1214 Planarity : 0.005 0.061 1295 Dihedral : 12.887 127.233 1234 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: 2.48 (0.26), residues: 991 helix: 1.85 (0.17), residues: 837 sheet: None (None), residues: 0 loop : 0.71 (0.56), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP a 212 HIS 0.005 0.002 HIS a 158 PHE 0.022 0.002 PHE a 99 TYR 0.021 0.001 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 72 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 73 MET cc_start: 0.6267 (mmp) cc_final: 0.5919 (mmp) REVERT: a 231 PHE cc_start: 0.7252 (t80) cc_final: 0.7052 (t80) REVERT: 3 85 LEU cc_start: 0.7799 (tp) cc_final: 0.7573 (tt) REVERT: 4 75 MET cc_start: 0.7597 (tmm) cc_final: 0.7225 (tmm) REVERT: 9 10 THR cc_start: 0.7972 (t) cc_final: 0.7743 (t) REVERT: 9 21 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6488 (mpp) outliers start: 7 outliers final: 4 residues processed: 68 average time/residue: 0.1570 time to fit residues: 16.0020 Evaluate side-chains 71 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 7 residue 75 MET 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 68 optimal weight: 0.0170 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 0.1980 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 7709 Z= 0.252 Angle : 0.615 8.757 10500 Z= 0.304 Chirality : 0.040 0.132 1214 Planarity : 0.005 0.060 1295 Dihedral : 12.386 129.843 1234 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.33 % Allowed : 14.48 % Favored : 84.19 % 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 (0.26), residues: 991 helix: 2.14 (0.17), residues: 837 sheet: None (None), residues: 0 loop : 0.65 (0.54), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 212 HIS 0.005 0.002 HIS a 158 PHE 0.018 0.001 PHE a 99 TYR 0.022 0.001 TYR a 145 ARG 0.002 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 75 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.818 Fit side-chains REVERT: a 62 VAL cc_start: 0.7759 (OUTLIER) cc_final: 0.7424 (t) REVERT: a 73 MET cc_start: 0.6300 (mmp) cc_final: 0.6084 (mmp) REVERT: 1 50 GLN cc_start: 0.7346 (pt0) cc_final: 0.7019 (pt0) REVERT: 2 75 MET cc_start: 0.6727 (tmm) cc_final: 0.6257 (ttp) REVERT: 4 75 MET cc_start: 0.7597 (tmm) cc_final: 0.7210 (tmm) REVERT: 8 71 ASN cc_start: 0.6608 (OUTLIER) cc_final: 0.6278 (m-40) REVERT: 9 10 THR cc_start: 0.7951 (t) cc_final: 0.7734 (t) outliers start: 9 outliers final: 1 residues processed: 72 average time/residue: 0.1676 time to fit residues: 17.5247 Evaluate side-chains 68 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain 8 residue 71 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7709 Z= 0.281 Angle : 0.617 9.149 10500 Z= 0.307 Chirality : 0.041 0.136 1214 Planarity : 0.004 0.059 1295 Dihedral : 12.098 132.055 1234 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.77 % Allowed : 14.62 % Favored : 83.60 % 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: 2.90 (0.25), residues: 991 helix: 2.16 (0.17), residues: 835 sheet: None (None), residues: 0 loop : 0.73 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP a 212 HIS 0.005 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 80 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: a 62 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7529 (t) REVERT: 1 50 GLN cc_start: 0.7354 (pt0) cc_final: 0.7138 (pt0) REVERT: 2 75 MET cc_start: 0.6795 (tmm) cc_final: 0.6562 (ttp) REVERT: 4 75 MET cc_start: 0.7566 (tmm) cc_final: 0.7205 (tmm) REVERT: 8 71 ASN cc_start: 0.6715 (OUTLIER) cc_final: 0.6385 (m-40) REVERT: 9 10 THR cc_start: 0.7992 (t) cc_final: 0.7770 (t) outliers start: 12 outliers final: 5 residues processed: 75 average time/residue: 0.1661 time to fit residues: 18.5467 Evaluate side-chains 74 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 83 MET 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 8 residue 21 MET Chi-restraints excluded: chain 8 residue 71 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.5980 chunk 56 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7709 Z= 0.305 Angle : 0.633 8.194 10500 Z= 0.316 Chirality : 0.042 0.150 1214 Planarity : 0.005 0.059 1295 Dihedral : 11.888 131.449 1234 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.48 % Allowed : 15.66 % Favored : 82.87 % 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: 2.84 (0.25), residues: 991 helix: 2.13 (0.17), residues: 835 sheet: None (None), residues: 0 loop : 0.64 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP a 212 HIS 0.005 0.002 HIS a 158 PHE 0.016 0.002 PHE a 206 TYR 0.019 0.001 TYR a 145 ARG 0.002 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 79 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: a 52 LYS cc_start: 0.6950 (tptp) cc_final: 0.6559 (mmmt) REVERT: a 62 VAL cc_start: 0.7866 (OUTLIER) cc_final: 0.7572 (t) REVERT: 1 50 GLN cc_start: 0.7308 (pt0) cc_final: 0.7084 (pt0) REVERT: 1 78 PHE cc_start: 0.6748 (m-10) cc_final: 0.6489 (m-10) REVERT: 2 75 MET cc_start: 0.6824 (tmm) cc_final: 0.6500 (ttp) REVERT: 7 21 MET cc_start: 0.7053 (mmm) cc_final: 0.6718 (mpp) REVERT: 8 71 ASN cc_start: 0.6692 (OUTLIER) cc_final: 0.6369 (m-40) REVERT: 9 10 THR cc_start: 0.7985 (t) cc_final: 0.7758 (t) outliers start: 10 outliers final: 6 residues processed: 74 average time/residue: 0.1593 time to fit residues: 17.3265 Evaluate side-chains 76 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 83 MET 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 8 residue 21 MET Chi-restraints excluded: chain 8 residue 71 ASN Chi-restraints excluded: chain 8 residue 72 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 0.1980 chunk 96 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 0.0470 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.3678 ------------------------------------------------------------------------------- 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** 9 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.2961 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= 0.218 Angle : 0.592 8.290 10500 Z= 0.293 Chirality : 0.040 0.139 1214 Planarity : 0.004 0.060 1295 Dihedral : 11.378 130.661 1234 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.48 % Allowed : 16.69 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.25), residues: 991 helix: 2.38 (0.17), residues: 834 sheet: None (None), residues: 0 loop : 0.48 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 212 HIS 0.004 0.001 HIS a 158 PHE 0.013 0.001 PHE 4 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 75 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: a 52 LYS cc_start: 0.6993 (tptp) cc_final: 0.6599 (mmmt) REVERT: a 135 LEU cc_start: 0.8100 (tp) cc_final: 0.7864 (tp) REVERT: 1 10 THR cc_start: 0.8440 (m) cc_final: 0.8227 (t) REVERT: 1 50 GLN cc_start: 0.7317 (pt0) cc_final: 0.7066 (pt0) REVERT: 1 78 PHE cc_start: 0.6636 (m-10) cc_final: 0.6216 (m-10) REVERT: 4 54 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6543 (m-10) REVERT: 4 75 MET cc_start: 0.7539 (tmm) cc_final: 0.7307 (tmm) REVERT: 7 21 MET cc_start: 0.7021 (mmm) cc_final: 0.6706 (mpp) REVERT: 8 71 ASN cc_start: 0.6661 (OUTLIER) cc_final: 0.6328 (m-40) REVERT: 9 10 THR cc_start: 0.7944 (t) cc_final: 0.7734 (t) outliers start: 10 outliers final: 3 residues processed: 70 average time/residue: 0.1662 time to fit residues: 17.1862 Evaluate side-chains 69 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain 1 residue 21 MET Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 8 residue 71 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 0.3980 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.3015 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= 0.258 Angle : 0.608 8.152 10500 Z= 0.303 Chirality : 0.041 0.139 1214 Planarity : 0.004 0.060 1295 Dihedral : 11.253 129.879 1234 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.89 % Allowed : 17.73 % Favored : 81.39 % 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: 3.04 (0.25), residues: 991 helix: 2.31 (0.17), residues: 835 sheet: None (None), residues: 0 loop : 0.43 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP a 212 HIS 0.004 0.001 HIS a 158 PHE 0.014 0.001 PHE 4 74 TYR 0.018 0.001 TYR a 145 ARG 0.003 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 75 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 52 LYS cc_start: 0.6965 (tptp) cc_final: 0.6651 (mmmt) REVERT: 1 78 PHE cc_start: 0.6800 (m-10) cc_final: 0.6598 (m-10) REVERT: 4 75 MET cc_start: 0.7535 (tmm) cc_final: 0.7249 (tmm) REVERT: 6 21 MET cc_start: 0.6652 (mtp) cc_final: 0.6397 (mtm) REVERT: 8 71 ASN cc_start: 0.6650 (OUTLIER) cc_final: 0.6366 (m-40) REVERT: 9 10 THR cc_start: 0.7969 (t) cc_final: 0.7756 (t) outliers start: 6 outliers final: 4 residues processed: 73 average time/residue: 0.1646 time to fit residues: 17.6219 Evaluate side-chains 73 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain 1 residue 21 MET Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 8 residue 71 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7709 Z= 0.252 Angle : 0.615 7.858 10500 Z= 0.307 Chirality : 0.041 0.143 1214 Planarity : 0.004 0.060 1295 Dihedral : 11.104 130.951 1234 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.18 % Allowed : 18.32 % Favored : 80.50 % 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: 3.02 (0.25), residues: 991 helix: 2.28 (0.17), residues: 837 sheet: None (None), residues: 0 loop : 0.51 (0.53), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP a 212 HIS 0.004 0.001 HIS a 158 PHE 0.015 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 75 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 75 MET cc_start: 0.7542 (tmm) cc_final: 0.7251 (tmm) REVERT: 5 21 MET cc_start: 0.7176 (mmm) cc_final: 0.6849 (mtp) REVERT: 7 21 MET cc_start: 0.7145 (mmm) cc_final: 0.6903 (mmm) REVERT: 8 71 ASN cc_start: 0.6669 (OUTLIER) cc_final: 0.6391 (m-40) REVERT: 9 10 THR cc_start: 0.7968 (t) cc_final: 0.7762 (t) REVERT: 9 21 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6452 (mpp) outliers start: 8 outliers final: 4 residues processed: 71 average time/residue: 0.1593 time to fit residues: 16.7763 Evaluate side-chains 72 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain 1 residue 21 MET Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 8 residue 71 ASN Chi-restraints excluded: chain 9 residue 21 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 99 optimal weight: 0.3980 chunk 91 optimal weight: 0.4980 chunk 79 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 0.2980 chunk 63 optimal weight: 0.4980 chunk 84 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.3241 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= 0.215 Angle : 0.608 10.169 10500 Z= 0.297 Chirality : 0.040 0.144 1214 Planarity : 0.004 0.060 1295 Dihedral : 10.911 130.653 1234 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.18 % Allowed : 19.05 % 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 (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: 3.16 (0.25), residues: 991 helix: 2.40 (0.17), residues: 836 sheet: None (None), residues: 0 loop : 0.39 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 212 HIS 0.004 0.001 HIS a 158 PHE 0.017 0.001 PHE 1 78 TYR 0.020 0.001 TYR a 145 ARG 0.002 0.000 ARG a 188 ********************** 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 73 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 135 LEU cc_start: 0.8088 (tp) cc_final: 0.7880 (tp) REVERT: 4 75 MET cc_start: 0.7531 (tmm) cc_final: 0.7215 (tmm) REVERT: 5 21 MET cc_start: 0.7176 (mmm) cc_final: 0.6813 (mtp) REVERT: 8 71 ASN cc_start: 0.6635 (OUTLIER) cc_final: 0.6388 (m-40) REVERT: 9 10 THR cc_start: 0.7949 (t) cc_final: 0.7743 (t) REVERT: 9 21 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6460 (mpp) outliers start: 8 outliers final: 4 residues processed: 70 average time/residue: 0.1640 time to fit residues: 16.9629 Evaluate side-chains 71 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain d residue 19 VAL Chi-restraints excluded: chain 1 residue 21 MET Chi-restraints excluded: chain 4 residue 77 LEU Chi-restraints excluded: chain 8 residue 71 ASN Chi-restraints excluded: chain 9 residue 21 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 0.0670 chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 69 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 57 optimal weight: 0.0670 overall best weight: 0.2256 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.153822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.142600 restraints weight = 8829.421| |-----------------------------------------------------------------------------| r_work (start): 0.3777 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: 3.76 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.3393 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= 0.186 Angle : 0.596 9.478 10500 Z= 0.289 Chirality : 0.040 0.148 1214 Planarity : 0.004 0.060 1295 Dihedral : 10.714 132.627 1234 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.03 % Allowed : 19.20 % 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 (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: 3.40 (0.25), residues: 991 helix: 2.58 (0.17), residues: 836 sheet: None (None), residues: 0 loop : 0.38 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 212 HIS 0.004 0.001 HIS a 158 PHE 0.014 0.001 PHE 1 74 TYR 0.020 0.001 TYR a 145 ARG 0.003 0.000 ARG a 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1587.86 seconds wall clock time: 29 minutes 30.33 seconds (1770.33 seconds total)