Starting phenix.real_space_refine on Thu Jun 4 04:06:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zkn_74378/06_2026/9zkn_74378.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zkn_74378/06_2026/9zkn_74378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zkn_74378/06_2026/9zkn_74378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zkn_74378/06_2026/9zkn_74378.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zkn_74378/06_2026/9zkn_74378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zkn_74378/06_2026/9zkn_74378.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 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 8 5.49 5 S 60 5.16 5 C 6808 2.51 5 N 1491 2.21 5 O 1733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 10100 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1034 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 130} 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: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1066 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1040 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1092 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 138} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1436 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1424 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1174 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 1, 'TRANS': 164} Chain breaks: 3 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 6, 'GLU:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "H" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1172 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 1, 'TRANS': 164} Chain breaks: 3 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 7, 'GLU:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 130 Unusual residues: {'OLC': 3, 'PLM': 2, 'POV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Unusual residues: {'OLC': 1, 'PLM': 3, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 121 Unusual residues: {'OLC': 2, 'PLM': 3, 'POV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 169 Unusual residues: {'OLC': 2, 'PLM': 3, 'POV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 2.65, per 1000 atoms: 0.26 Number of scatterers: 10100 At special positions: 0 Unit cell: (113.85, 114.675, 86.625, 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 60 16.00 P 8 15.00 O 1733 8.00 N 1491 7.00 C 6808 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.06 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 91 " distance=2.03 Simple disulfide: pdb=" SG CYS G 90 " - pdb=" SG CYS G 100 " distance=2.04 Simple disulfide: pdb=" SG CYS H 52 " - pdb=" SG CYS H 91 " distance=2.02 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 100 " distance=2.02 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: 1.00 Conformation dependent library (CDL) restraints added in 373.8 milliseconds 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2278 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 71.5% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 625 Processing helix chain 'A' and resid 788 through 813 removed outlier: 3.636A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.839A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 545 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 788 through 817 removed outlier: 4.090A pdb=" N VAL B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B 817 " --> pdb=" O GLU B 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 518 through 541 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 625 Processing helix chain 'C' and resid 788 through 813 removed outlier: 3.618A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.636A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 544 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 792 through 818 removed outlier: 3.693A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 128 removed outlier: 4.087A pdb=" N GLU E 126 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.687A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 210 removed outlier: 3.562A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 30 Processing helix chain 'F' and resid 92 through 105 Processing helix chain 'F' and resid 105 through 128 removed outlier: 3.600A pdb=" N ILE F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 162 Processing helix chain 'F' and resid 177 through 210 removed outlier: 3.610A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 40 Processing helix chain 'G' and resid 118 through 128 Processing helix chain 'G' and resid 128 through 149 removed outlier: 3.931A pdb=" N ARG G 149 " --> pdb=" O VAL G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 184 removed outlier: 4.379A pdb=" N LEU G 159 " --> pdb=" O ARG G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 231 removed outlier: 3.924A pdb=" N TYR G 206 " --> pdb=" O GLY G 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 41 Processing helix chain 'H' and resid 118 through 128 Processing helix chain 'H' and resid 128 through 148 removed outlier: 3.572A pdb=" N ILE H 132 " --> pdb=" O SER H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 183 Processing helix chain 'H' and resid 202 through 231 removed outlier: 3.721A pdb=" N TYR H 206 " --> pdb=" O GLY H 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 77 through 79 removed outlier: 3.540A pdb=" N THR E 59 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER E 36 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER E 175 " --> pdb=" O TYR E 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 66 through 68 Processing sheet with id=AA3, first strand: chain 'G' and resid 101 through 102 removed outlier: 4.406A pdb=" N VAL G 101 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE G 89 " --> pdb=" O VAL G 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 102 755 hydrogen bonds defined for protein. 2223 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: 1.81 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 2711 1.34 - 1.47: 3005 1.47 - 1.61: 4489 1.61 - 1.75: 0 1.75 - 1.88: 88 Bond restraints: 10293 Sorted by residual: bond pdb=" O12 POV A1003 " pdb=" P POV A1003 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.58e+00 bond pdb=" O12 POV C1003 " pdb=" P POV C1003 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.58e+00 bond pdb=" O12 POV D1004 " pdb=" P POV D1004 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" C11 POV E 401 " pdb=" O12 POV E 401 " ideal model delta sigma weight residual 1.408 1.459 -0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" C1 POV D1004 " pdb=" O11 POV D1004 " ideal model delta sigma weight residual 1.410 1.461 -0.051 2.00e-02 2.50e+03 6.49e+00 ... (remaining 10288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 13658 3.27 - 6.54: 131 6.54 - 9.81: 9 9.81 - 13.09: 2 13.09 - 16.36: 2 Bond angle restraints: 13802 Sorted by residual: angle pdb=" CA LEU F 12 " pdb=" CB LEU F 12 " pdb=" CG LEU F 12 " ideal model delta sigma weight residual 116.30 132.66 -16.36 3.50e+00 8.16e-02 2.18e+01 angle pdb=" CA CYS E 67 " pdb=" CB CYS E 67 " pdb=" SG CYS E 67 " ideal model delta sigma weight residual 114.40 125.08 -10.68 2.30e+00 1.89e-01 2.16e+01 angle pdb=" CA LEU F 120 " pdb=" CB LEU F 120 " pdb=" CG LEU F 120 " ideal model delta sigma weight residual 116.30 132.01 -15.71 3.50e+00 8.16e-02 2.01e+01 angle pdb=" N CYS E 67 " pdb=" CA CYS E 67 " pdb=" C CYS E 67 " ideal model delta sigma weight residual 108.76 114.70 -5.94 1.58e+00 4.01e-01 1.41e+01 angle pdb=" C SER A 540 " pdb=" N ARG A 541 " pdb=" CA ARG A 541 " ideal model delta sigma weight residual 122.24 116.56 5.68 1.57e+00 4.06e-01 1.31e+01 ... (remaining 13797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 5839 35.05 - 70.10: 93 70.10 - 105.15: 9 105.15 - 140.20: 19 140.20 - 175.25: 4 Dihedral angle restraints: 5964 sinusoidal: 2408 harmonic: 3556 Sorted by residual: dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 158.21 -65.21 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS E 67 " pdb=" SG CYS E 67 " pdb=" SG CYS E 77 " pdb=" CB CYS E 77 " ideal model delta sinusoidal sigma weight residual 93.00 42.21 50.79 1 1.00e+01 1.00e-02 3.53e+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 -2.64 175.25 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1145 0.046 - 0.092: 325 0.092 - 0.138: 75 0.138 - 0.184: 5 0.184 - 0.230: 5 Chirality restraints: 1555 Sorted by residual: chirality pdb=" CA CYS E 67 " pdb=" N CYS E 67 " pdb=" C CYS E 67 " pdb=" CB CYS E 67 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE G 89 " pdb=" CA ILE G 89 " pdb=" CG1 ILE G 89 " pdb=" CG2 ILE G 89 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB THR E 66 " pdb=" CA THR E 66 " pdb=" OG1 THR E 66 " pdb=" CG2 THR E 66 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1552 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 515 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.18e+00 pdb=" N PRO A 516 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 516 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 516 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 83 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.50e+00 pdb=" N PRO F 84 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO F 84 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 84 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 519 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO D 520 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 520 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 520 " -0.030 5.00e-02 4.00e+02 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 616 2.74 - 3.28: 10183 3.28 - 3.82: 16952 3.82 - 4.36: 19278 4.36 - 4.90: 34848 Nonbonded interactions: 81877 Sorted by model distance: nonbonded pdb=" OG1 THR G 82 " pdb=" O CYS G 90 " model vdw 2.196 3.040 nonbonded pdb=" O HIS E 82 " pdb=" NH2 ARG E 99 " model vdw 2.245 3.120 nonbonded pdb=" O VAL H 21 " pdb=" OG1 THR H 24 " model vdw 2.257 3.040 nonbonded pdb=" OG1 THR H 82 " pdb=" O CYS H 90 " model vdw 2.258 3.040 nonbonded pdb=" O ILE F 134 " pdb=" OG SER F 137 " model vdw 2.266 3.040 ... (remaining 81872 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 506 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 780 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 )) or resid 1003 through 1004 o \ r (resid 1005 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C \ 6 or name C7 or name O1 or name O2 )))) selection = (chain 'B' and (resid 510 or (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 784 \ and (name N or name CA or name C or name O or name CB )) or resid 785 through 7 \ 99 or resid 801 through 815 or (resid 816 through 817 and (name N or name CA or \ name C or name O or name CB )) or (resid 1002 and (name C1 or name C2 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or nam \ e C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C37 or name C38 or name C39 or name O11 or name O12 \ or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name \ P or name C310 or name C311 or name C312)) or resid 1003 through 1004)) selection = (chain 'C' and (resid 506 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 780 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 )) or (resid 1003 and (name C1 \ or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O3 \ 1 or name O32 or name P or name C310 or name C311 or name C312)) or resid 1004 o \ r (resid 1005 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C \ 6 or name C7 or name O1 or name O2 )))) selection = (chain 'D' and (resid 510 or (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 784 \ and (name N or name CA or name C or name O or name CB )) or resid 785 through 7 \ 99 or resid 801 through 817 or (resid 1004 and (name C1 or name C2 or name C21 o \ r name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name O11 or name O12 or \ name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P \ or name C310 or name C311 or name C312)) or resid 1005 through 1006)) } ncs_group { reference = (chain 'E' and (resid 4 through 77 or (resid 78 and (name N or name CA or name C \ or name O or name CB )) or resid 79 through 85 or (resid 86 through 91 and (nam \ e N or name CA or name C or name O or name CB )) or resid 92 through 401)) selection = (chain 'F' and (resid 4 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or resid 7 through 9 or (resid 10 and (name N or name CA \ or name C or name O or name CB )) or resid 11 through 210 or (resid 401 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name \ O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or \ name O32 or name P or name C210 or name C211 or name C310 or name C311 or name C \ 312 or name C313 or name C314 or name C315)))) } ncs_group { reference = (chain 'G' and (resid 19 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 87 or (resid 88 and (name N or nam \ e CA or name C or name O or name CB )) or resid 89 through 231)) selection = (chain 'H' and (resid 19 through 118 or (resid 119 and (name N or name CA or nam \ e C or name O or name CB )) or resid 120 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: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.810 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 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 : 0.006 0.073 10301 Z= 0.280 Angle : 0.813 16.356 13818 Z= 0.390 Chirality : 0.045 0.230 1555 Planarity : 0.005 0.062 1630 Dihedral : 16.687 175.252 3662 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 1.37 (0.23), residues: 1201 helix: 1.84 (0.16), residues: 880 sheet: -4.57 (0.96), residues: 10 loop : -1.69 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 595 TYR 0.019 0.002 TYR F 128 PHE 0.030 0.002 PHE B 574 TRP 0.032 0.002 TRP F 178 HIS 0.009 0.002 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.28 (10293) covalent geometry : angle 0.80724 / 0.39 (13802) SS BOND : bond 0.00981 / 0.52 ( 8) SS BOND : angle 2.88858 / 1.79 ( 16) hydrogen bonds : bond 0.09572 / 6.49 ( 755) hydrogen bonds : angle 4.60951 / 3.31 ( 2223) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 619 PHE cc_start: 0.6948 (m-80) cc_final: 0.6735 (m-10) REVERT: A 623 GLU cc_start: 0.6542 (mm-30) cc_final: 0.6295 (pt0) REVERT: B 545 ARG cc_start: 0.6482 (mmt180) cc_final: 0.6157 (mmt180) REVERT: C 541 ARG cc_start: 0.6359 (mmm160) cc_final: 0.5888 (mmm160) REVERT: C 566 GLU cc_start: 0.7365 (pm20) cc_final: 0.7061 (pm20) REVERT: C 590 ARG cc_start: 0.7805 (mtm180) cc_final: 0.7462 (mtm-85) REVERT: C 623 GLU cc_start: 0.7442 (tp30) cc_final: 0.6572 (tt0) REVERT: C 625 MET cc_start: 0.7532 (mtm) cc_final: 0.7293 (mtm) REVERT: D 516 SER cc_start: 0.7546 (m) cc_final: 0.7290 (m) REVERT: D 527 MET cc_start: 0.7045 (ttp) cc_final: 0.6777 (ttt) REVERT: E 23 LEU cc_start: 0.5386 (mt) cc_final: 0.5121 (mp) REVERT: E 117 MET cc_start: 0.3906 (mmm) cc_final: 0.3596 (mtp) REVERT: E 192 MET cc_start: 0.4584 (mtp) cc_final: 0.3873 (mpm) REVERT: F 73 PHE cc_start: 0.4757 (m-80) cc_final: 0.4319 (m-10) REVERT: G 218 ILE cc_start: 0.7073 (tp) cc_final: 0.6836 (tp) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.4227 time to fit residues: 90.1228 Evaluate side-chains 147 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 GLN C 565 ASN D 575 ASN F 9 GLN ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.191959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.140126 restraints weight = 10889.144| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.95 r_work: 0.3414 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10301 Z= 0.214 Angle : 0.621 9.371 13818 Z= 0.314 Chirality : 0.041 0.159 1555 Planarity : 0.005 0.053 1630 Dihedral : 15.777 166.540 1844 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.39 % Allowed : 8.37 % Favored : 87.24 % 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: 1.90 (0.24), residues: 1201 helix: 2.32 (0.17), residues: 878 sheet: -2.53 (1.01), residues: 20 loop : -1.82 (0.31), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 99 TYR 0.013 0.002 TYR B 523 PHE 0.016 0.002 PHE A 619 TRP 0.020 0.002 TRP F 178 HIS 0.012 0.002 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.21 (10293) covalent geometry : angle 0.61793 / 0.31 (13802) SS BOND : bond 0.00629 / 0.34 ( 8) SS BOND : angle 1.77719 / 1.04 ( 16) hydrogen bonds : bond 0.04414 / 2.91 ( 755) hydrogen bonds : angle 3.81839 / 2.76 ( 2223) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7810 (tpt170) cc_final: 0.7560 (mmt-90) REVERT: B 586 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7260 (mmp-170) REVERT: C 519 TYR cc_start: 0.8494 (t80) cc_final: 0.8291 (t80) REVERT: C 541 ARG cc_start: 0.7093 (mmm160) cc_final: 0.6645 (mmm160) REVERT: C 623 GLU cc_start: 0.8619 (tp30) cc_final: 0.7984 (tt0) REVERT: E 23 LEU cc_start: 0.6139 (mt) cc_final: 0.5880 (mp) REVERT: E 117 MET cc_start: 0.4755 (mmm) cc_final: 0.3776 (mtm) REVERT: E 192 MET cc_start: 0.5745 (mtp) cc_final: 0.4879 (mpm) REVERT: F 99 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.5925 (mpp-170) REVERT: F 202 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7057 (pt) outliers start: 42 outliers final: 17 residues processed: 176 average time/residue: 0.4682 time to fit residues: 89.9545 Evaluate side-chains 159 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 586 ARG Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 583 GLN Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 150 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 113 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 50 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.194991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.144007 restraints weight = 10949.071| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.88 r_work: 0.3459 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10301 Z= 0.115 Angle : 0.479 8.862 13818 Z= 0.248 Chirality : 0.037 0.141 1555 Planarity : 0.004 0.047 1630 Dihedral : 13.931 130.686 1844 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.35 % Allowed : 12.97 % Favored : 83.68 % 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: 2.48 (0.24), residues: 1201 helix: 2.78 (0.17), residues: 880 sheet: -2.64 (0.92), residues: 26 loop : -1.69 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 590 TYR 0.011 0.001 TYR F 174 PHE 0.012 0.001 PHE D 546 TRP 0.014 0.001 TRP F 178 HIS 0.008 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (10293) covalent geometry : angle 0.47757 / 0.25 (13802) SS BOND : bond 0.00429 / 0.23 ( 8) SS BOND : angle 1.14682 / 0.69 ( 16) hydrogen bonds : bond 0.03698 / 2.42 ( 755) hydrogen bonds : angle 3.44160 / 2.48 ( 2223) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: B 545 ARG cc_start: 0.7441 (mmt180) cc_final: 0.7220 (mmt180) REVERT: C 541 ARG cc_start: 0.6996 (mmm160) cc_final: 0.6593 (mmm160) REVERT: C 623 GLU cc_start: 0.8637 (tp30) cc_final: 0.8071 (tt0) REVERT: E 23 LEU cc_start: 0.6189 (mt) cc_final: 0.5955 (mp) REVERT: E 117 MET cc_start: 0.4680 (mmm) cc_final: 0.4050 (mtp) REVERT: E 192 MET cc_start: 0.5725 (mtp) cc_final: 0.4876 (mpm) REVERT: F 202 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7046 (pt) REVERT: G 102 LYS cc_start: 0.7154 (pttt) cc_final: 0.6862 (pttp) outliers start: 32 outliers final: 15 residues processed: 161 average time/residue: 0.4732 time to fit residues: 83.1407 Evaluate side-chains 152 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 225 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 93 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.194751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.143228 restraints weight = 11045.275| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.95 r_work: 0.3448 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10301 Z= 0.116 Angle : 0.478 10.471 13818 Z= 0.246 Chirality : 0.037 0.189 1555 Planarity : 0.003 0.045 1630 Dihedral : 13.507 125.472 1844 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.56 % Allowed : 13.49 % Favored : 82.95 % 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: 2.69 (0.24), residues: 1201 helix: 2.95 (0.17), residues: 880 sheet: -2.65 (0.91), residues: 26 loop : -1.65 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 590 TYR 0.016 0.001 TYR H 226 PHE 0.018 0.001 PHE E 18 TRP 0.012 0.001 TRP F 178 HIS 0.007 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (10293) covalent geometry : angle 0.47709 / 0.25 (13802) SS BOND : bond 0.00737 / 0.36 ( 8) SS BOND : angle 1.15533 / 0.63 ( 16) hydrogen bonds : bond 0.03597 / 2.35 ( 755) hydrogen bonds : angle 3.36420 / 2.42 ( 2223) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7769 (mmt-90) cc_final: 0.7527 (mmt-90) REVERT: B 545 ARG cc_start: 0.7418 (mmt180) cc_final: 0.7174 (mmt180) REVERT: C 541 ARG cc_start: 0.6970 (mmm160) cc_final: 0.6585 (mmm160) REVERT: C 623 GLU cc_start: 0.8663 (tp30) cc_final: 0.8032 (tt0) REVERT: D 586 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7237 (mmp-170) REVERT: E 23 LEU cc_start: 0.6103 (mt) cc_final: 0.5877 (mp) REVERT: E 65 ARG cc_start: 0.5389 (mtm110) cc_final: 0.5086 (mtt90) REVERT: E 117 MET cc_start: 0.4664 (mmm) cc_final: 0.4113 (mtp) REVERT: E 192 MET cc_start: 0.5649 (mtp) cc_final: 0.4806 (mpm) REVERT: F 202 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7040 (pt) REVERT: G 82 THR cc_start: 0.7367 (OUTLIER) cc_final: 0.7102 (t) REVERT: G 102 LYS cc_start: 0.7141 (pttt) cc_final: 0.6858 (pttp) REVERT: H 34 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7376 (mp) outliers start: 34 outliers final: 15 residues processed: 166 average time/residue: 0.5200 time to fit residues: 93.4504 Evaluate side-chains 154 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 586 ARG Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 225 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 74 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 9 GLN G 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.193929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142520 restraints weight = 10982.984| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.06 r_work: 0.3438 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10301 Z= 0.123 Angle : 0.482 13.439 13818 Z= 0.248 Chirality : 0.037 0.199 1555 Planarity : 0.003 0.046 1630 Dihedral : 13.451 122.592 1844 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.29 % Allowed : 13.81 % Favored : 81.90 % 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: 2.72 (0.24), residues: 1201 helix: 3.00 (0.17), residues: 876 sheet: -2.63 (0.89), residues: 26 loop : -1.69 (0.32), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 590 TYR 0.011 0.001 TYR C 519 PHE 0.021 0.001 PHE E 201 TRP 0.011 0.001 TRP F 64 HIS 0.006 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (10293) covalent geometry : angle 0.48106 / 0.25 (13802) SS BOND : bond 0.00457 / 0.24 ( 8) SS BOND : angle 1.07314 / 0.58 ( 16) hydrogen bonds : bond 0.03649 / 2.39 ( 755) hydrogen bonds : angle 3.37070 / 2.44 ( 2223) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.402 Fit side-chains REVERT: A 541 ARG cc_start: 0.7809 (mmt-90) cc_final: 0.7601 (mmt-90) REVERT: B 545 ARG cc_start: 0.7434 (mmt180) cc_final: 0.7212 (mmt180) REVERT: C 541 ARG cc_start: 0.6983 (mmm160) cc_final: 0.6602 (mmm160) REVERT: C 623 GLU cc_start: 0.8716 (tp30) cc_final: 0.8147 (tt0) REVERT: D 586 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7308 (mmp-170) REVERT: E 23 LEU cc_start: 0.6269 (mt) cc_final: 0.5983 (mp) REVERT: E 26 ILE cc_start: 0.6830 (OUTLIER) cc_final: 0.6466 (mm) REVERT: E 65 ARG cc_start: 0.5380 (mtm110) cc_final: 0.5164 (mtt90) REVERT: E 117 MET cc_start: 0.4671 (mmm) cc_final: 0.4101 (mtp) REVERT: E 192 MET cc_start: 0.5695 (mtp) cc_final: 0.4834 (mpm) REVERT: F 113 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7884 (mp) REVERT: F 202 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7019 (pt) REVERT: G 82 THR cc_start: 0.7432 (OUTLIER) cc_final: 0.7141 (t) REVERT: G 102 LYS cc_start: 0.7149 (pttt) cc_final: 0.6878 (pttp) REVERT: H 34 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7500 (mp) outliers start: 41 outliers final: 20 residues processed: 164 average time/residue: 0.5011 time to fit residues: 89.1038 Evaluate side-chains 159 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 583 GLN Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 586 ARG Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 225 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 40 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.194371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.144209 restraints weight = 11046.606| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.14 r_work: 0.3420 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10301 Z= 0.116 Angle : 0.493 15.311 13818 Z= 0.247 Chirality : 0.037 0.192 1555 Planarity : 0.003 0.045 1630 Dihedral : 13.250 119.488 1844 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.66 % Allowed : 15.27 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.24), residues: 1201 helix: 3.06 (0.17), residues: 876 sheet: -2.61 (0.88), residues: 26 loop : -1.65 (0.32), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 590 TYR 0.011 0.001 TYR C 519 PHE 0.014 0.001 PHE B 531 TRP 0.012 0.001 TRP F 64 HIS 0.006 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (10293) covalent geometry : angle 0.49165 / 0.25 (13802) SS BOND : bond 0.00354 / 0.19 ( 8) SS BOND : angle 1.14912 / 0.65 ( 16) hydrogen bonds : bond 0.03560 / 2.33 ( 755) hydrogen bonds : angle 3.33633 / 2.40 ( 2223) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7856 (mmt-90) cc_final: 0.7652 (mmt-90) REVERT: B 545 ARG cc_start: 0.7406 (mmt180) cc_final: 0.7192 (mmt180) REVERT: C 541 ARG cc_start: 0.6945 (mmm160) cc_final: 0.6582 (mmm160) REVERT: C 566 GLU cc_start: 0.7703 (pm20) cc_final: 0.7215 (pm20) REVERT: C 623 GLU cc_start: 0.8714 (tp30) cc_final: 0.8093 (tt0) REVERT: D 586 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7234 (mmp-170) REVERT: E 31 ASP cc_start: 0.7507 (m-30) cc_final: 0.7301 (m-30) REVERT: E 117 MET cc_start: 0.4629 (mmm) cc_final: 0.4062 (mtp) REVERT: E 192 MET cc_start: 0.5635 (mtp) cc_final: 0.4779 (mpm) REVERT: F 202 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7069 (pt) REVERT: G 82 THR cc_start: 0.7389 (OUTLIER) cc_final: 0.7099 (t) REVERT: G 102 LYS cc_start: 0.7099 (pttt) cc_final: 0.6841 (pttp) REVERT: H 34 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7378 (mp) outliers start: 35 outliers final: 21 residues processed: 157 average time/residue: 0.4993 time to fit residues: 85.1875 Evaluate side-chains 154 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 586 ARG Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 225 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 100 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.192878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141873 restraints weight = 10938.658| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.06 r_work: 0.3427 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10301 Z= 0.138 Angle : 0.507 13.923 13818 Z= 0.258 Chirality : 0.038 0.198 1555 Planarity : 0.003 0.047 1630 Dihedral : 13.611 119.068 1844 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.66 % Allowed : 15.48 % Favored : 80.86 % 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: 2.67 (0.24), residues: 1201 helix: 2.90 (0.17), residues: 884 sheet: -2.42 (0.95), residues: 24 loop : -1.65 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 590 TYR 0.013 0.001 TYR H 199 PHE 0.017 0.001 PHE E 18 TRP 0.009 0.001 TRP F 64 HIS 0.006 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10293) covalent geometry : angle 0.50498 / 0.26 (13802) SS BOND : bond 0.00492 / 0.25 ( 8) SS BOND : angle 1.31188 / 0.69 ( 16) hydrogen bonds : bond 0.03750 / 2.46 ( 755) hydrogen bonds : angle 3.42265 / 2.47 ( 2223) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7811 (mmt-90) cc_final: 0.7597 (mmt-90) REVERT: B 545 ARG cc_start: 0.7428 (mmt180) cc_final: 0.7225 (mmt180) REVERT: C 541 ARG cc_start: 0.7040 (mmm160) cc_final: 0.6663 (mmm160) REVERT: C 566 GLU cc_start: 0.7693 (pm20) cc_final: 0.7190 (pm20) REVERT: C 590 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.8056 (mtm110) REVERT: C 623 GLU cc_start: 0.8655 (tp30) cc_final: 0.8092 (tt0) REVERT: D 586 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7282 (mmp-170) REVERT: E 26 ILE cc_start: 0.6707 (OUTLIER) cc_final: 0.6348 (mm) REVERT: E 65 ARG cc_start: 0.5176 (mtt90) cc_final: 0.4331 (mtm110) REVERT: E 117 MET cc_start: 0.4656 (mmm) cc_final: 0.4079 (mtp) REVERT: E 192 MET cc_start: 0.5694 (mtp) cc_final: 0.4853 (mpm) REVERT: F 202 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7015 (pt) REVERT: G 82 THR cc_start: 0.7451 (OUTLIER) cc_final: 0.7176 (t) REVERT: G 102 LYS cc_start: 0.7135 (pttt) cc_final: 0.6879 (pttp) REVERT: H 34 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7440 (mp) outliers start: 35 outliers final: 22 residues processed: 162 average time/residue: 0.4941 time to fit residues: 86.9412 Evaluate side-chains 158 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 586 ARG Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 225 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 98 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.194076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.143759 restraints weight = 11050.241| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.20 r_work: 0.3406 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10301 Z= 0.119 Angle : 0.510 14.092 13818 Z= 0.254 Chirality : 0.037 0.198 1555 Planarity : 0.003 0.047 1630 Dihedral : 13.220 114.818 1844 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.35 % Allowed : 15.79 % Favored : 80.86 % 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: 2.77 (0.25), residues: 1201 helix: 2.99 (0.17), residues: 884 sheet: -2.70 (0.88), residues: 26 loop : -1.61 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 590 TYR 0.013 0.001 TYR H 226 PHE 0.018 0.001 PHE B 531 TRP 0.010 0.001 TRP G 203 HIS 0.005 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10293) covalent geometry : angle 0.50831 / 0.25 (13802) SS BOND : bond 0.00462 / 0.23 ( 8) SS BOND : angle 1.19444 / 0.61 ( 16) hydrogen bonds : bond 0.03611 / 2.37 ( 755) hydrogen bonds : angle 3.37889 / 2.44 ( 2223) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7848 (mmt-90) cc_final: 0.7631 (mmt-90) REVERT: C 541 ARG cc_start: 0.6978 (mmm160) cc_final: 0.6618 (mmm160) REVERT: C 566 GLU cc_start: 0.7682 (pm20) cc_final: 0.7155 (pm20) REVERT: C 590 ARG cc_start: 0.8435 (mtm-85) cc_final: 0.8128 (mtm110) REVERT: C 623 GLU cc_start: 0.8719 (tp30) cc_final: 0.8111 (tt0) REVERT: D 586 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7296 (mmp-170) REVERT: E 23 LEU cc_start: 0.6469 (mp) cc_final: 0.6049 (mp) REVERT: E 26 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6369 (mm) REVERT: E 65 ARG cc_start: 0.5089 (mtt90) cc_final: 0.4248 (mtm110) REVERT: E 117 MET cc_start: 0.4650 (mmm) cc_final: 0.4073 (mtp) REVERT: E 192 MET cc_start: 0.5674 (mtp) cc_final: 0.4837 (mpm) REVERT: F 202 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.6977 (pt) REVERT: G 82 THR cc_start: 0.7421 (OUTLIER) cc_final: 0.7132 (t) REVERT: G 102 LYS cc_start: 0.7141 (pttt) cc_final: 0.6886 (pttp) REVERT: H 34 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7447 (mp) outliers start: 32 outliers final: 21 residues processed: 155 average time/residue: 0.4967 time to fit residues: 83.4714 Evaluate side-chains 155 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 586 ARG Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 225 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 6 optimal weight: 0.0980 chunk 82 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 112 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 119 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.195060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.144288 restraints weight = 10971.137| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.99 r_work: 0.3450 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 10301 Z= 0.108 Angle : 0.487 13.421 13818 Z= 0.244 Chirality : 0.037 0.197 1555 Planarity : 0.003 0.047 1630 Dihedral : 12.810 109.763 1844 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.56 % Allowed : 15.59 % Favored : 80.86 % 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: 2.91 (0.25), residues: 1201 helix: 3.15 (0.17), residues: 877 sheet: -2.77 (0.87), residues: 26 loop : -1.64 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 590 TYR 0.016 0.001 TYR H 199 PHE 0.018 0.001 PHE B 531 TRP 0.015 0.001 TRP F 64 HIS 0.005 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (10293) covalent geometry : angle 0.48565 / 0.24 (13802) SS BOND : bond 0.00408 / 0.21 ( 8) SS BOND : angle 1.06295 / 0.57 ( 16) hydrogen bonds : bond 0.03476 / 2.27 ( 755) hydrogen bonds : angle 3.30384 / 2.38 ( 2223) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.340 Fit side-chains REVERT: B 586 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7153 (mmp-170) REVERT: C 541 ARG cc_start: 0.6919 (mmm160) cc_final: 0.6578 (mmm160) REVERT: C 566 GLU cc_start: 0.7628 (pm20) cc_final: 0.7125 (pm20) REVERT: C 590 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8098 (mtm110) REVERT: C 623 GLU cc_start: 0.8680 (tp30) cc_final: 0.7992 (pt0) REVERT: D 586 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7207 (mmp-170) REVERT: E 23 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6071 (mp) REVERT: E 26 ILE cc_start: 0.6672 (OUTLIER) cc_final: 0.6334 (mm) REVERT: E 117 MET cc_start: 0.4622 (mmm) cc_final: 0.4042 (mtp) REVERT: E 192 MET cc_start: 0.5588 (mtp) cc_final: 0.4748 (mpm) REVERT: F 202 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.6908 (pt) REVERT: G 82 THR cc_start: 0.7317 (OUTLIER) cc_final: 0.7010 (t) REVERT: G 102 LYS cc_start: 0.7120 (pttt) cc_final: 0.6856 (pttp) REVERT: H 34 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7366 (mp) outliers start: 34 outliers final: 22 residues processed: 157 average time/residue: 0.5056 time to fit residues: 86.1473 Evaluate side-chains 161 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 586 ARG Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 586 ARG Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 225 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 84 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 0.0670 chunk 118 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 114 optimal weight: 0.0470 chunk 27 optimal weight: 0.1980 chunk 98 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.196236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.145194 restraints weight = 10831.805| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.93 r_work: 0.3482 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 10301 Z= 0.101 Angle : 0.494 13.114 13818 Z= 0.244 Chirality : 0.036 0.206 1555 Planarity : 0.003 0.047 1630 Dihedral : 12.276 101.115 1844 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.03 % Allowed : 16.42 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.24), residues: 1201 helix: 3.24 (0.17), residues: 878 sheet: None (None), residues: 0 loop : -1.72 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 590 TYR 0.012 0.001 TYR H 226 PHE 0.021 0.001 PHE B 531 TRP 0.019 0.001 TRP G 203 HIS 0.005 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (10293) covalent geometry : angle 0.49285 / 0.24 (13802) SS BOND : bond 0.00374 / 0.19 ( 8) SS BOND : angle 0.98842 / 0.53 ( 16) hydrogen bonds : bond 0.03348 / 2.19 ( 755) hydrogen bonds : angle 3.23900 / 2.33 ( 2223) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: B 586 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7130 (mmp-170) REVERT: C 541 ARG cc_start: 0.6789 (mmm160) cc_final: 0.6485 (mmm160) REVERT: C 566 GLU cc_start: 0.7602 (pm20) cc_final: 0.7093 (pm20) REVERT: C 590 ARG cc_start: 0.8380 (mtm-85) cc_final: 0.8075 (mtm110) REVERT: C 623 GLU cc_start: 0.8706 (tp30) cc_final: 0.8030 (pt0) REVERT: D 586 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7175 (mmp-170) REVERT: E 23 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6114 (mp) REVERT: E 26 ILE cc_start: 0.6806 (OUTLIER) cc_final: 0.6465 (mm) REVERT: E 117 MET cc_start: 0.4670 (mmm) cc_final: 0.4086 (mtp) REVERT: E 192 MET cc_start: 0.5665 (mtp) cc_final: 0.4829 (mpm) REVERT: F 202 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.6986 (pt) REVERT: G 82 THR cc_start: 0.7313 (OUTLIER) cc_final: 0.7015 (t) REVERT: G 102 LYS cc_start: 0.7140 (pttt) cc_final: 0.6878 (pttm) REVERT: H 34 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7399 (mp) outliers start: 29 outliers final: 20 residues processed: 160 average time/residue: 0.5239 time to fit residues: 90.7310 Evaluate side-chains 154 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 586 ARG Chi-restraints excluded: chain C residue 519 TYR Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 586 ARG Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 225 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 41 optimal weight: 0.2980 chunk 108 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.193070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142841 restraints weight = 11029.383| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.13 r_work: 0.3395 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10301 Z= 0.139 Angle : 0.525 13.025 13818 Z= 0.263 Chirality : 0.038 0.201 1555 Planarity : 0.003 0.048 1630 Dihedral : 12.983 102.783 1844 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.45 % Allowed : 16.21 % Favored : 80.33 % 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: 2.80 (0.24), residues: 1201 helix: 3.04 (0.17), residues: 877 sheet: -2.22 (1.04), residues: 20 loop : -1.67 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 65 TYR 0.017 0.002 TYR H 199 PHE 0.025 0.001 PHE B 531 TRP 0.018 0.001 TRP G 203 HIS 0.006 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (10293) covalent geometry : angle 0.52438 / 0.26 (13802) SS BOND : bond 0.00424 / 0.22 ( 8) SS BOND : angle 1.13521 / 0.61 ( 16) hydrogen bonds : bond 0.03737 / 2.45 ( 755) hydrogen bonds : angle 3.42820 / 2.48 ( 2223) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4136.70 seconds wall clock time: 71 minutes 13.08 seconds (4273.08 seconds total)