Starting phenix.real_space_refine on Thu Jun 4 02:10:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zkt_74384/06_2026/9zkt_74384.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zkt_74384/06_2026/9zkt_74384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zkt_74384/06_2026/9zkt_74384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zkt_74384/06_2026/9zkt_74384.map" model { file = "/net/cci-nas-00/data/ceres_data/9zkt_74384/06_2026/9zkt_74384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zkt_74384/06_2026/9zkt_74384.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 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 P 3 5.49 5 S 62 5.16 5 C 6497 2.51 5 N 1424 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9580 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1028 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1071 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1147 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1038 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 981 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "F" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1189 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1190 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 1, 'TRANS': 164} Chain breaks: 3 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "H" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1218 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 1, 'TRANS': 168} Chain breaks: 3 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "M" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 283 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 123 Unusual residues: {'OLC': 2, 'PLM': 2, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {'OLC': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'OLC': 3, 'PLM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 108 Unusual residues: {'OLC': 2, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "M" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Time building chain proxies: 2.59, per 1000 atoms: 0.27 Number of scatterers: 9580 At special positions: 0 Unit cell: (113.025, 108.075, 95.7, 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) S 62 16.00 P 3 15.00 O 1594 8.00 N 1424 7.00 C 6497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS G 90 " - pdb=" SG CYS G 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 52 " - pdb=" SG CYS H 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 100 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 361.5 milliseconds 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 3 sheets defined 78.3% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 518 through 541 Processing helix chain 'A' and resid 569 through 581 Processing helix chain 'A' and resid 591 through 625 Processing helix chain 'A' and resid 788 through 813 removed outlier: 3.678A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.538A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 547 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.915A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 518 through 542 removed outlier: 3.545A pdb=" N PHE C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 625 Processing helix chain 'C' and resid 784 through 787 Processing helix chain 'C' and resid 788 through 820 removed outlier: 3.565A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.771A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 547 removed outlier: 3.954A pdb=" N SER D 547 " --> pdb=" O VAL D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 788 through 819 removed outlier: 3.664A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 36 Processing helix chain 'E' and resid 57 through 85 Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 87 through 108 Proline residue: E 96 - end of helix removed outlier: 3.733A pdb=" N ARG E 108 " --> pdb=" O ARG E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 159 removed outlier: 3.701A pdb=" N SER E 159 " --> pdb=" O TYR E 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 38 removed outlier: 3.613A pdb=" N SER F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE F 38 " --> pdb=" O LEU F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 85 removed outlier: 4.374A pdb=" N VAL F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) Proline residue: F 70 - end of helix Processing helix chain 'F' and resid 87 through 107 removed outlier: 3.696A pdb=" N LEU F 91 " --> pdb=" O GLU F 87 " (cutoff:3.500A) Proline residue: F 96 - end of helix Processing helix chain 'F' and resid 126 through 157 removed outlier: 3.852A pdb=" N TYR F 130 " --> pdb=" O ASP F 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 41 Processing helix chain 'G' and resid 118 through 128 Processing helix chain 'G' and resid 128 through 147 Processing helix chain 'G' and resid 156 through 185 removed outlier: 3.522A pdb=" N GLY G 160 " --> pdb=" O ASN G 156 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY G 185 " --> pdb=" O SER G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 231 removed outlier: 3.779A pdb=" N TYR G 206 " --> pdb=" O GLY G 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 41 Processing helix chain 'H' and resid 118 through 128 Processing helix chain 'H' and resid 128 through 148 removed outlier: 3.699A pdb=" N ILE H 132 " --> pdb=" O SER H 128 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 185 removed outlier: 4.100A pdb=" N LEU H 159 " --> pdb=" O ARG H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 231 removed outlier: 3.620A pdb=" N TYR H 206 " --> pdb=" O GLY H 202 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU H 221 " --> pdb=" O VAL H 217 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG H 231 " --> pdb=" O ILE H 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 261 through 298 Processing sheet with id=AA1, first strand: chain 'G' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.678A pdb=" N SER H 200 " --> pdb=" O TYR H 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 81 through 84 removed outlier: 3.968A pdb=" N LEU H 81 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS H 83 " --> pdb=" O CYS H 90 " (cutoff:3.500A) 759 hydrogen bonds defined for protein. 2250 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1482 1.33 - 1.45: 2801 1.45 - 1.58: 5414 1.58 - 1.70: 6 1.70 - 1.83: 85 Bond restraints: 9788 Sorted by residual: bond pdb=" O12 POV G 501 " pdb=" P POV G 501 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" O12 POV D1003 " pdb=" P POV D1003 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.44e+00 bond pdb=" O12 POV A1003 " pdb=" P POV A1003 " ideal model delta sigma weight residual 1.657 1.608 0.049 2.00e-02 2.50e+03 6.01e+00 bond pdb=" C11 POV A1003 " pdb=" O12 POV A1003 " ideal model delta sigma weight residual 1.408 1.457 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" C11 POV D1003 " pdb=" O12 POV D1003 " ideal model delta sigma weight residual 1.408 1.455 -0.047 2.00e-02 2.50e+03 5.57e+00 ... (remaining 9783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 12845 2.21 - 4.42: 276 4.42 - 6.63: 52 6.63 - 8.84: 13 8.84 - 11.05: 1 Bond angle restraints: 13187 Sorted by residual: angle pdb=" C ALA F 125 " pdb=" N ASP F 126 " pdb=" CA ASP F 126 " ideal model delta sigma weight residual 121.54 132.59 -11.05 1.91e+00 2.74e-01 3.35e+01 angle pdb=" N VAL F 120 " pdb=" CA VAL F 120 " pdb=" C VAL F 120 " ideal model delta sigma weight residual 109.29 103.79 5.50 1.42e+00 4.96e-01 1.50e+01 angle pdb=" C LYS F 55 " pdb=" N ASN F 56 " pdb=" CA ASN F 56 " ideal model delta sigma weight residual 121.58 114.29 7.29 1.95e+00 2.63e-01 1.40e+01 angle pdb=" CB GLU C 809 " pdb=" CG GLU C 809 " pdb=" CD GLU C 809 " ideal model delta sigma weight residual 112.60 118.43 -5.83 1.70e+00 3.46e-01 1.18e+01 angle pdb=" C MET B 585 " pdb=" N ARG B 586 " pdb=" CA ARG B 586 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 ... (remaining 13182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 5473 35.02 - 70.05: 105 70.05 - 105.07: 10 105.07 - 140.09: 11 140.09 - 175.11: 3 Dihedral angle restraints: 5602 sinusoidal: 2154 harmonic: 3448 Sorted by residual: dihedral pdb=" CB CYS H 90 " pdb=" SG CYS H 90 " pdb=" SG CYS H 100 " pdb=" CB CYS H 100 " ideal model delta sinusoidal sigma weight residual -86.00 -44.68 -41.32 1 1.00e+01 1.00e-02 2.39e+01 dihedral pdb=" C3 POV D1003 " pdb=" C31 POV D1003 " pdb=" O31 POV D1003 " pdb=" C32 POV D1003 " ideal model delta sinusoidal sigma weight residual 172.61 -2.50 175.11 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 POV G 501 " pdb=" C31 POV G 501 " pdb=" O31 POV G 501 " pdb=" C32 POV G 501 " ideal model delta sinusoidal sigma weight residual 172.61 -0.52 173.13 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1131 0.045 - 0.091: 317 0.091 - 0.136: 55 0.136 - 0.181: 12 0.181 - 0.226: 5 Chirality restraints: 1520 Sorted by residual: chirality pdb=" CG LEU M 285 " pdb=" CB LEU M 285 " pdb=" CD1 LEU M 285 " pdb=" CD2 LEU M 285 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA VAL F 120 " pdb=" N VAL F 120 " pdb=" C VAL F 120 " pdb=" CB VAL F 120 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CG LEU C 804 " pdb=" CB LEU C 804 " pdb=" CD1 LEU C 804 " pdb=" CD2 LEU C 804 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.47e-01 ... (remaining 1517 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 515 " 0.053 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO A 516 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 516 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 516 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 546 " -0.010 2.00e-02 2.50e+03 1.89e-02 6.22e+00 pdb=" CG PHE D 546 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE D 546 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE D 546 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE D 546 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 546 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 546 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 515 " 0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO C 516 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 516 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 516 " 0.033 5.00e-02 4.00e+02 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1705 2.77 - 3.30: 9303 3.30 - 3.83: 16228 3.83 - 4.37: 18034 4.37 - 4.90: 32036 Nonbonded interactions: 77306 Sorted by model distance: nonbonded pdb=" OH TYR F 10 " pdb=" OE1 GLU F 87 " model vdw 2.233 3.040 nonbonded pdb=" O LEU F 16 " pdb=" OG SER F 19 " model vdw 2.287 3.040 nonbonded pdb=" NH1 ARG A 624 " pdb=" O VAL D 626 " model vdw 2.317 3.120 nonbonded pdb=" OG1 THR G 82 " pdb=" O CYS G 90 " model vdw 2.322 3.040 nonbonded pdb=" O LEU E 16 " pdb=" OG SER E 19 " model vdw 2.327 3.040 ... (remaining 77301 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 'A' and (resid 507 through 543 or (resid 565 and (name N or name CA or na \ me C or name O or name CB )) or resid 566 through 581 or resid 583 through 624 o \ r resid 781 through 795 or resid 797 through 811 or (resid 812 through 813 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and ((resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 547 or resid 569 through 585 or resid 587 through 628 o \ r resid 785 through 799 or resid 801 through 817)) selection = (chain 'C' and (resid 507 through 543 or (resid 565 and (name N or name CA or na \ me C or name O or name CB )) or resid 566 through 581 or resid 583 through 624 o \ r resid 781 through 795 or resid 797 through 811 or (resid 812 through 813 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 585 or resid 587 through 628 or resid 785 through 799 o \ r resid 801 through 817)) } ncs_group { reference = (chain 'G' and resid 18 through 231) selection = (chain 'H' and (resid 18 through 51 or resid 80 through 231)) } 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: 3.970 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.850 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 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 : 0.005 0.055 9791 Z= 0.243 Angle : 0.791 11.054 13193 Z= 0.396 Chirality : 0.044 0.226 1520 Planarity : 0.005 0.080 1549 Dihedral : 16.337 175.113 3373 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.24), residues: 1147 helix: 1.70 (0.16), residues: 906 sheet: -1.74 (1.00), residues: 10 loop : -2.35 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 594 TYR 0.032 0.001 TYR E 151 PHE 0.041 0.002 PHE D 546 TRP 0.009 0.001 TRP F 136 HIS 0.012 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.24 ( 9788) covalent geometry : angle 0.79011 / 0.40 (13187) SS BOND : bond 0.00391 / 0.20 ( 3) SS BOND : angle 1.50181 / 0.90 ( 6) hydrogen bonds : bond 0.10071 / 6.70 ( 759) hydrogen bonds : angle 4.54431 / 3.30 ( 2250) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 590 ARG cc_start: 0.8563 (ttm-80) cc_final: 0.8321 (ttm-80) REVERT: A 623 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7004 (mt-10) REVERT: C 590 ARG cc_start: 0.8084 (mtp-110) cc_final: 0.7207 (mtm-85) REVERT: D 527 MET cc_start: 0.7079 (mmt) cc_final: 0.6654 (mmp) REVERT: D 545 ARG cc_start: 0.5559 (tpp80) cc_final: 0.4408 (ttp80) REVERT: D 594 ARG cc_start: 0.7541 (mtm110) cc_final: 0.6806 (mtp85) REVERT: F 31 PHE cc_start: 0.6547 (m-80) cc_final: 0.5441 (m-80) REVERT: F 35 ARG cc_start: 0.6874 (tpt170) cc_final: 0.5843 (mpt180) REVERT: F 38 PHE cc_start: 0.6007 (p90) cc_final: 0.5803 (t80) REVERT: F 63 LEU cc_start: 0.7085 (tp) cc_final: 0.6652 (tp) REVERT: F 66 LYS cc_start: 0.6889 (mmmt) cc_final: 0.6168 (pttt) REVERT: G 144 CYS cc_start: 0.8712 (m) cc_final: 0.8276 (m) REVERT: H 35 MET cc_start: 0.6085 (tpt) cc_final: 0.5703 (mmm) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.0952 time to fit residues: 26.0876 Evaluate side-chains 156 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.0770 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 overall best weight: 1.1144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 HIS ** H 183 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 = 0.4054 r_free = 0.4054 target = 0.181004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.131893 restraints weight = 11884.633| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.22 r_work: 0.3392 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9791 Z= 0.148 Angle : 0.567 9.873 13193 Z= 0.292 Chirality : 0.038 0.202 1520 Planarity : 0.004 0.071 1549 Dihedral : 13.054 164.778 1615 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.72 % Allowed : 7.86 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.25), residues: 1147 helix: 2.36 (0.16), residues: 913 sheet: -1.91 (1.42), residues: 15 loop : -2.02 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 594 TYR 0.012 0.001 TYR H 43 PHE 0.038 0.001 PHE M 273 TRP 0.006 0.001 TRP E 103 HIS 0.007 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 9788) covalent geometry : angle 0.56722 / 0.29 (13187) SS BOND : bond 0.00213 / 0.11 ( 3) SS BOND : angle 0.76536 / 0.47 ( 6) hydrogen bonds : bond 0.04359 / 2.87 ( 759) hydrogen bonds : angle 3.71273 / 2.65 ( 2250) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 623 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7505 (mt-10) REVERT: C 590 ARG cc_start: 0.8713 (mtp-110) cc_final: 0.7990 (mtm-85) REVERT: D 527 MET cc_start: 0.8244 (mmt) cc_final: 0.7930 (mmp) REVERT: D 537 SER cc_start: 0.8855 (t) cc_final: 0.8503 (m) REVERT: D 594 ARG cc_start: 0.8088 (mtm110) cc_final: 0.7519 (mtt-85) REVERT: F 31 PHE cc_start: 0.6953 (m-80) cc_final: 0.5816 (m-80) REVERT: F 35 ARG cc_start: 0.6877 (tpt170) cc_final: 0.6012 (mpt180) REVERT: F 38 PHE cc_start: 0.6197 (p90) cc_final: 0.5791 (t80) REVERT: F 63 LEU cc_start: 0.7355 (tp) cc_final: 0.6923 (tp) REVERT: F 66 LYS cc_start: 0.7335 (mmmt) cc_final: 0.6467 (pttt) REVERT: F 102 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6981 (mm) REVERT: G 88 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7255 (mtm-85) REVERT: G 144 CYS cc_start: 0.8976 (m) cc_final: 0.8516 (m) REVERT: H 125 ARG cc_start: 0.7877 (tpt90) cc_final: 0.7569 (tpt90) REVERT: H 174 ILE cc_start: 0.8551 (mm) cc_final: 0.8266 (mt) outliers start: 16 outliers final: 11 residues processed: 171 average time/residue: 0.1045 time to fit residues: 24.5176 Evaluate side-chains 165 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 173 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 110 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 172 ASN ** H 183 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 = 0.4046 r_free = 0.4046 target = 0.180204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.131590 restraints weight = 11773.156| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.14 r_work: 0.3375 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9791 Z= 0.141 Angle : 0.525 7.266 13193 Z= 0.272 Chirality : 0.038 0.179 1520 Planarity : 0.004 0.059 1549 Dihedral : 11.645 156.022 1615 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.94 % Allowed : 9.90 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.25), residues: 1147 helix: 2.60 (0.16), residues: 915 sheet: -3.61 (1.06), residues: 20 loop : -1.86 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 594 TYR 0.015 0.001 TYR F 100 PHE 0.029 0.001 PHE M 273 TRP 0.009 0.001 TRP F 26 HIS 0.009 0.002 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9788) covalent geometry : angle 0.52500 / 0.27 (13187) SS BOND : bond 0.00226 / 0.11 ( 3) SS BOND : angle 0.31957 / 0.20 ( 6) hydrogen bonds : bond 0.04234 / 2.79 ( 759) hydrogen bonds : angle 3.58455 / 2.56 ( 2250) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 623 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7874 (tt0) REVERT: B 812 ILE cc_start: 0.8572 (mt) cc_final: 0.8354 (mm) REVERT: C 590 ARG cc_start: 0.8717 (mtp-110) cc_final: 0.7976 (mtm-85) REVERT: D 527 MET cc_start: 0.8194 (mmt) cc_final: 0.7859 (mmp) REVERT: D 537 SER cc_start: 0.8834 (t) cc_final: 0.8511 (m) REVERT: D 541 PHE cc_start: 0.8426 (t80) cc_final: 0.8196 (t80) REVERT: D 594 ARG cc_start: 0.8101 (mtm110) cc_final: 0.7563 (mtt-85) REVERT: E 146 PHE cc_start: 0.7033 (t80) cc_final: 0.6265 (t80) REVERT: F 29 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6554 (mp) REVERT: F 31 PHE cc_start: 0.7015 (m-80) cc_final: 0.5919 (m-80) REVERT: F 38 PHE cc_start: 0.6131 (p90) cc_final: 0.5663 (t80) REVERT: F 63 LEU cc_start: 0.7353 (tp) cc_final: 0.6937 (tp) REVERT: F 66 LYS cc_start: 0.7371 (mmmt) cc_final: 0.6549 (pttt) REVERT: G 144 CYS cc_start: 0.8959 (m) cc_final: 0.8469 (m) REVERT: H 174 ILE cc_start: 0.8526 (mm) cc_final: 0.8319 (mt) outliers start: 18 outliers final: 13 residues processed: 170 average time/residue: 0.0997 time to fit residues: 23.6621 Evaluate side-chains 165 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 173 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 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 = 0.4048 r_free = 0.4048 target = 0.180382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.132006 restraints weight = 11874.675| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.15 r_work: 0.3376 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9791 Z= 0.126 Angle : 0.502 9.685 13193 Z= 0.259 Chirality : 0.037 0.196 1520 Planarity : 0.003 0.056 1549 Dihedral : 11.230 143.264 1615 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.26 % Allowed : 11.19 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.25), residues: 1147 helix: 2.82 (0.16), residues: 917 sheet: -3.47 (1.05), residues: 20 loop : -1.79 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 594 TYR 0.014 0.001 TYR F 72 PHE 0.021 0.001 PHE M 273 TRP 0.007 0.001 TRP E 88 HIS 0.009 0.002 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9788) covalent geometry : angle 0.50179 / 0.26 (13187) SS BOND : bond 0.00177 / 0.09 ( 3) SS BOND : angle 0.43566 / 0.25 ( 6) hydrogen bonds : bond 0.04037 / 2.66 ( 759) hydrogen bonds : angle 3.46419 / 2.47 ( 2250) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 566 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8074 (pt0) REVERT: A 623 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7846 (tt0) REVERT: B 812 ILE cc_start: 0.8572 (mt) cc_final: 0.8361 (mm) REVERT: C 590 ARG cc_start: 0.8714 (mtp-110) cc_final: 0.7964 (mtm-85) REVERT: D 527 MET cc_start: 0.8183 (mmt) cc_final: 0.7882 (mmp) REVERT: D 537 SER cc_start: 0.8849 (t) cc_final: 0.8507 (m) REVERT: D 594 ARG cc_start: 0.8077 (mtm110) cc_final: 0.7491 (mtt-85) REVERT: E 146 PHE cc_start: 0.6953 (t80) cc_final: 0.6064 (t80) REVERT: F 10 TYR cc_start: 0.8674 (m-80) cc_final: 0.8157 (m-80) REVERT: F 31 PHE cc_start: 0.6945 (m-80) cc_final: 0.5507 (m-80) REVERT: F 35 ARG cc_start: 0.6800 (tpt170) cc_final: 0.6017 (mtt-85) REVERT: F 38 PHE cc_start: 0.6078 (p90) cc_final: 0.5838 (t80) REVERT: F 63 LEU cc_start: 0.7302 (tp) cc_final: 0.6807 (tp) REVERT: F 66 LYS cc_start: 0.7312 (mmmt) cc_final: 0.6508 (pttt) REVERT: F 133 LYS cc_start: 0.7445 (mmtm) cc_final: 0.7192 (mmtm) REVERT: G 144 CYS cc_start: 0.8898 (m) cc_final: 0.8383 (m) outliers start: 21 outliers final: 14 residues processed: 167 average time/residue: 0.1013 time to fit residues: 23.9417 Evaluate side-chains 168 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 129 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 74 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 51 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 787 ASN ** H 183 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 = 0.4002 r_free = 0.4002 target = 0.175896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.127321 restraints weight = 11982.188| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.16 r_work: 0.3335 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9791 Z= 0.177 Angle : 0.556 11.727 13193 Z= 0.286 Chirality : 0.039 0.202 1520 Planarity : 0.004 0.054 1549 Dihedral : 11.682 130.377 1615 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.01 % Allowed : 12.59 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.25), residues: 1147 helix: 2.71 (0.16), residues: 914 sheet: -3.62 (1.08), residues: 20 loop : -1.90 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 594 TYR 0.013 0.001 TYR G 43 PHE 0.028 0.001 PHE D 541 TRP 0.008 0.001 TRP E 88 HIS 0.009 0.002 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 9788) covalent geometry : angle 0.55652 / 0.29 (13187) SS BOND : bond 0.00143 / 0.07 ( 3) SS BOND : angle 0.50765 / 0.28 ( 6) hydrogen bonds : bond 0.04431 / 2.90 ( 759) hydrogen bonds : angle 3.59226 / 2.55 ( 2250) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8231 (pt0) REVERT: A 623 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7835 (tt0) REVERT: B 594 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7665 (mmt-90) REVERT: C 590 ARG cc_start: 0.8724 (mtp-110) cc_final: 0.7949 (mtm-85) REVERT: D 527 MET cc_start: 0.8158 (mmt) cc_final: 0.7890 (mmt) REVERT: D 537 SER cc_start: 0.8860 (t) cc_final: 0.8548 (m) REVERT: D 594 ARG cc_start: 0.8101 (mtm110) cc_final: 0.7590 (mtt-85) REVERT: E 146 PHE cc_start: 0.6952 (t80) cc_final: 0.6074 (t80) REVERT: F 10 TYR cc_start: 0.8728 (m-80) cc_final: 0.8283 (m-80) REVERT: F 29 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6467 (mp) REVERT: F 31 PHE cc_start: 0.6964 (m-80) cc_final: 0.5527 (m-80) REVERT: F 35 ARG cc_start: 0.6832 (tpt170) cc_final: 0.6143 (mtt-85) REVERT: F 38 PHE cc_start: 0.5998 (p90) cc_final: 0.5776 (t80) REVERT: F 66 LYS cc_start: 0.7262 (mmmt) cc_final: 0.6460 (pttt) REVERT: F 133 LYS cc_start: 0.7481 (mmtm) cc_final: 0.7182 (mmtm) outliers start: 28 outliers final: 23 residues processed: 168 average time/residue: 0.1034 time to fit residues: 24.2334 Evaluate side-chains 174 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 91 CYS Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 173 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 15 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 70 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 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 = 0.4039 r_free = 0.4039 target = 0.179340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131189 restraints weight = 11809.690| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.13 r_work: 0.3370 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9791 Z= 0.122 Angle : 0.503 11.032 13193 Z= 0.259 Chirality : 0.037 0.214 1520 Planarity : 0.003 0.053 1549 Dihedral : 11.139 123.842 1615 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.69 % Allowed : 13.56 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.25), residues: 1147 helix: 2.97 (0.16), residues: 914 sheet: -2.52 (1.30), residues: 15 loop : -1.88 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 594 TYR 0.007 0.001 TYR G 43 PHE 0.025 0.001 PHE D 541 TRP 0.007 0.001 TRP E 88 HIS 0.009 0.002 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9788) covalent geometry : angle 0.50256 / 0.26 (13187) SS BOND : bond 0.00124 / 0.06 ( 3) SS BOND : angle 0.42995 / 0.24 ( 6) hydrogen bonds : bond 0.03998 / 2.62 ( 759) hydrogen bonds : angle 3.43408 / 2.44 ( 2250) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8294 (pt0) REVERT: A 623 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7807 (tt0) REVERT: B 594 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7638 (mmt-90) REVERT: C 523 MET cc_start: 0.8552 (ttp) cc_final: 0.8298 (ttm) REVERT: C 590 ARG cc_start: 0.8720 (mtp-110) cc_final: 0.7947 (mtm-85) REVERT: D 527 MET cc_start: 0.8159 (mmt) cc_final: 0.7869 (mmt) REVERT: D 537 SER cc_start: 0.8773 (t) cc_final: 0.8457 (m) REVERT: D 594 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7505 (mtt-85) REVERT: E 146 PHE cc_start: 0.6979 (t80) cc_final: 0.5984 (t80) REVERT: F 10 TYR cc_start: 0.8674 (m-80) cc_final: 0.8219 (m-80) REVERT: F 29 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6431 (mp) REVERT: F 31 PHE cc_start: 0.6971 (m-80) cc_final: 0.5555 (m-80) REVERT: F 35 ARG cc_start: 0.6905 (tpt170) cc_final: 0.6213 (mtt-85) REVERT: F 38 PHE cc_start: 0.5981 (p90) cc_final: 0.5734 (t80) REVERT: F 66 LYS cc_start: 0.7244 (mmmt) cc_final: 0.6382 (pttt) REVERT: F 133 LYS cc_start: 0.7496 (mmtm) cc_final: 0.7181 (mmtm) REVERT: G 136 ILE cc_start: 0.8110 (mt) cc_final: 0.7817 (mp) outliers start: 25 outliers final: 17 residues processed: 179 average time/residue: 0.1045 time to fit residues: 25.9864 Evaluate side-chains 174 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 91 CYS Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain M residue 284 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 100 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 183 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 = 0.4014 r_free = 0.4014 target = 0.177076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128542 restraints weight = 11892.939| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.17 r_work: 0.3343 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9791 Z= 0.142 Angle : 0.521 10.878 13193 Z= 0.269 Chirality : 0.038 0.223 1520 Planarity : 0.003 0.053 1549 Dihedral : 11.178 121.923 1615 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.69 % Allowed : 13.78 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.06 (0.25), residues: 1147 helix: 2.92 (0.16), residues: 914 sheet: -2.36 (1.31), residues: 15 loop : -1.90 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 229 TYR 0.009 0.001 TYR H 43 PHE 0.027 0.001 PHE D 541 TRP 0.007 0.001 TRP E 88 HIS 0.009 0.002 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9788) covalent geometry : angle 0.52125 / 0.27 (13187) SS BOND : bond 0.00142 / 0.07 ( 3) SS BOND : angle 0.54948 / 0.30 ( 6) hydrogen bonds : bond 0.04127 / 2.70 ( 759) hydrogen bonds : angle 3.47993 / 2.47 ( 2250) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 623 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7884 (tt0) REVERT: B 594 ARG cc_start: 0.8085 (mmm-85) cc_final: 0.7654 (mmt-90) REVERT: C 523 MET cc_start: 0.8638 (ttp) cc_final: 0.8401 (ttm) REVERT: C 590 ARG cc_start: 0.8735 (mtp-110) cc_final: 0.7991 (mtm-85) REVERT: D 527 MET cc_start: 0.8225 (mmt) cc_final: 0.7949 (mmt) REVERT: D 537 SER cc_start: 0.8836 (t) cc_final: 0.8513 (m) REVERT: D 594 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7661 (mtt-85) REVERT: E 146 PHE cc_start: 0.7013 (t80) cc_final: 0.5999 (t80) REVERT: F 10 TYR cc_start: 0.8728 (m-80) cc_final: 0.8299 (m-80) REVERT: F 29 ILE cc_start: 0.6690 (OUTLIER) cc_final: 0.6409 (mp) REVERT: F 31 PHE cc_start: 0.7002 (m-80) cc_final: 0.5917 (m-80) REVERT: F 38 PHE cc_start: 0.6014 (p90) cc_final: 0.5531 (t80) REVERT: F 66 LYS cc_start: 0.7203 (mmmt) cc_final: 0.6393 (pttt) REVERT: F 133 LYS cc_start: 0.7511 (mmtm) cc_final: 0.7190 (mmtm) REVERT: G 136 ILE cc_start: 0.8191 (mt) cc_final: 0.7890 (mp) outliers start: 25 outliers final: 20 residues processed: 168 average time/residue: 0.1045 time to fit residues: 24.3066 Evaluate side-chains 169 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 91 CYS Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain M residue 284 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 75 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 83 optimal weight: 0.0970 chunk 61 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 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 = 0.4011 r_free = 0.4011 target = 0.176635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129019 restraints weight = 11866.854| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.10 r_work: 0.3358 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9791 Z= 0.141 Angle : 0.524 11.182 13193 Z= 0.268 Chirality : 0.038 0.227 1520 Planarity : 0.003 0.053 1549 Dihedral : 11.154 119.902 1615 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.80 % Allowed : 14.21 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.25), residues: 1147 helix: 2.94 (0.16), residues: 915 sheet: -2.25 (1.30), residues: 15 loop : -1.96 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 229 TYR 0.008 0.001 TYR G 43 PHE 0.028 0.001 PHE D 541 TRP 0.007 0.001 TRP E 88 HIS 0.008 0.002 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 9788) covalent geometry : angle 0.52358 / 0.27 (13187) SS BOND : bond 0.00132 / 0.07 ( 3) SS BOND : angle 0.58557 / 0.32 ( 6) hydrogen bonds : bond 0.04100 / 2.68 ( 759) hydrogen bonds : angle 3.45759 / 2.46 ( 2250) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 623 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7734 (tm-30) REVERT: B 594 ARG cc_start: 0.8082 (mmm-85) cc_final: 0.7649 (mmt-90) REVERT: C 523 MET cc_start: 0.8583 (ttp) cc_final: 0.8339 (ttm) REVERT: C 590 ARG cc_start: 0.8711 (mtp-110) cc_final: 0.7922 (mtm-85) REVERT: D 527 MET cc_start: 0.8168 (mmt) cc_final: 0.7883 (mmt) REVERT: D 537 SER cc_start: 0.8811 (t) cc_final: 0.8498 (m) REVERT: D 594 ARG cc_start: 0.8111 (mtm110) cc_final: 0.7633 (mtt-85) REVERT: E 146 PHE cc_start: 0.6989 (t80) cc_final: 0.5996 (t80) REVERT: F 10 TYR cc_start: 0.8686 (m-80) cc_final: 0.8276 (m-80) REVERT: F 29 ILE cc_start: 0.6720 (OUTLIER) cc_final: 0.6427 (mp) REVERT: F 31 PHE cc_start: 0.7007 (m-80) cc_final: 0.5933 (m-80) REVERT: F 38 PHE cc_start: 0.5982 (p90) cc_final: 0.5480 (t80) REVERT: F 66 LYS cc_start: 0.7174 (mmmt) cc_final: 0.6357 (pttt) REVERT: F 133 LYS cc_start: 0.7537 (mmtm) cc_final: 0.7216 (mmtm) REVERT: G 136 ILE cc_start: 0.8149 (mt) cc_final: 0.7866 (mp) REVERT: G 144 CYS cc_start: 0.9126 (m) cc_final: 0.8503 (m) outliers start: 26 outliers final: 22 residues processed: 170 average time/residue: 0.1080 time to fit residues: 25.1858 Evaluate side-chains 173 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 91 CYS Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain M residue 284 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 30.0000 chunk 84 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 172 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 = 0.4002 r_free = 0.4002 target = 0.175855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127573 restraints weight = 11805.891| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.13 r_work: 0.3343 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9791 Z= 0.158 Angle : 0.536 11.625 13193 Z= 0.276 Chirality : 0.038 0.230 1520 Planarity : 0.003 0.053 1549 Dihedral : 11.350 119.618 1615 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.91 % Allowed : 14.53 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.25), residues: 1147 helix: 2.88 (0.16), residues: 915 sheet: -2.12 (1.31), residues: 15 loop : -2.00 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 65 TYR 0.011 0.001 TYR F 72 PHE 0.026 0.001 PHE D 541 TRP 0.006 0.001 TRP G 44 HIS 0.008 0.002 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 9788) covalent geometry : angle 0.53572 / 0.28 (13187) SS BOND : bond 0.00164 / 0.08 ( 3) SS BOND : angle 0.67645 / 0.36 ( 6) hydrogen bonds : bond 0.04246 / 2.77 ( 759) hydrogen bonds : angle 3.50764 / 2.50 ( 2250) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 623 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7730 (tm-30) REVERT: C 523 MET cc_start: 0.8557 (ttp) cc_final: 0.8310 (ttm) REVERT: C 590 ARG cc_start: 0.8720 (mtp-110) cc_final: 0.7920 (mtm-85) REVERT: D 527 MET cc_start: 0.8156 (mmt) cc_final: 0.7867 (mmt) REVERT: D 537 SER cc_start: 0.8800 (t) cc_final: 0.8550 (m) REVERT: D 594 ARG cc_start: 0.8133 (mtm110) cc_final: 0.7646 (mtt-85) REVERT: E 146 PHE cc_start: 0.7058 (t80) cc_final: 0.6081 (t80) REVERT: F 10 TYR cc_start: 0.8697 (m-80) cc_final: 0.8276 (m-80) REVERT: F 29 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6481 (mp) REVERT: F 31 PHE cc_start: 0.7022 (m-80) cc_final: 0.5630 (m-80) REVERT: F 35 ARG cc_start: 0.6890 (tpt170) cc_final: 0.6304 (mtt180) REVERT: F 38 PHE cc_start: 0.6044 (p90) cc_final: 0.5673 (t80) REVERT: F 66 LYS cc_start: 0.7238 (mmmt) cc_final: 0.6416 (pttt) REVERT: F 133 LYS cc_start: 0.7518 (mmtm) cc_final: 0.7197 (mmtm) REVERT: G 136 ILE cc_start: 0.8150 (mt) cc_final: 0.7863 (mp) outliers start: 27 outliers final: 23 residues processed: 171 average time/residue: 0.1072 time to fit residues: 25.3788 Evaluate side-chains 176 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 91 CYS Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain M residue 284 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 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 = 0.4012 r_free = 0.4012 target = 0.176703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.129274 restraints weight = 11826.656| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.09 r_work: 0.3362 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9791 Z= 0.131 Angle : 0.517 11.461 13193 Z= 0.265 Chirality : 0.037 0.243 1520 Planarity : 0.003 0.053 1549 Dihedral : 11.044 115.725 1615 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.69 % Allowed : 15.18 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.25), residues: 1147 helix: 3.01 (0.16), residues: 914 sheet: -2.06 (1.29), residues: 15 loop : -1.99 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 266 TYR 0.008 0.001 TYR H 43 PHE 0.026 0.001 PHE D 541 TRP 0.006 0.001 TRP B 551 HIS 0.008 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9788) covalent geometry : angle 0.51649 / 0.27 (13187) SS BOND : bond 0.00144 / 0.07 ( 3) SS BOND : angle 0.61139 / 0.33 ( 6) hydrogen bonds : bond 0.04058 / 2.65 ( 759) hydrogen bonds : angle 3.44774 / 2.45 ( 2250) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 623 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7705 (tm-30) REVERT: C 523 MET cc_start: 0.8574 (ttp) cc_final: 0.8329 (ttm) REVERT: C 590 ARG cc_start: 0.8709 (mtp-110) cc_final: 0.7928 (mtm-85) REVERT: D 527 MET cc_start: 0.8150 (mmt) cc_final: 0.7860 (mmt) REVERT: D 537 SER cc_start: 0.8756 (t) cc_final: 0.8508 (m) REVERT: D 594 ARG cc_start: 0.8123 (mtm110) cc_final: 0.7647 (mtt-85) REVERT: E 146 PHE cc_start: 0.6973 (t80) cc_final: 0.5959 (t80) REVERT: F 10 TYR cc_start: 0.8642 (m-80) cc_final: 0.8232 (m-80) REVERT: F 29 ILE cc_start: 0.6649 (OUTLIER) cc_final: 0.6344 (mp) REVERT: F 31 PHE cc_start: 0.6941 (m-80) cc_final: 0.5917 (m-80) REVERT: F 35 ARG cc_start: 0.6895 (tpt170) cc_final: 0.6311 (mtt180) REVERT: F 38 PHE cc_start: 0.5999 (p90) cc_final: 0.5668 (t80) REVERT: F 66 LYS cc_start: 0.7172 (mmmt) cc_final: 0.6350 (pttt) REVERT: F 133 LYS cc_start: 0.7532 (mmtm) cc_final: 0.7204 (mmtm) REVERT: G 136 ILE cc_start: 0.8148 (mt) cc_final: 0.7865 (mp) outliers start: 25 outliers final: 22 residues processed: 170 average time/residue: 0.1072 time to fit residues: 25.0810 Evaluate side-chains 172 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 827 ILE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 91 CYS Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain M residue 284 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 29 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 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 = 0.4010 r_free = 0.4010 target = 0.176654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128578 restraints weight = 11920.895| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.13 r_work: 0.3353 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9791 Z= 0.140 Angle : 0.522 11.536 13193 Z= 0.268 Chirality : 0.038 0.235 1520 Planarity : 0.003 0.053 1549 Dihedral : 10.950 113.828 1615 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.48 % Allowed : 14.96 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.25), residues: 1147 helix: 2.99 (0.16), residues: 915 sheet: -1.99 (1.30), residues: 15 loop : -1.96 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 229 TYR 0.018 0.001 TYR F 72 PHE 0.018 0.001 PHE D 541 TRP 0.006 0.001 TRP B 551 HIS 0.009 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 9788) covalent geometry : angle 0.52243 / 0.27 (13187) SS BOND : bond 0.00126 / 0.06 ( 3) SS BOND : angle 0.65144 / 0.34 ( 6) hydrogen bonds : bond 0.04114 / 2.69 ( 759) hydrogen bonds : angle 3.45013 / 2.46 ( 2250) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3206.05 seconds wall clock time: 55 minutes 29.42 seconds (3329.42 seconds total)