Starting phenix.real_space_refine on Mon Aug 25 19:21:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j03_35882/08_2025/8j03_35882_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j03_35882/08_2025/8j03_35882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j03_35882/08_2025/8j03_35882_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j03_35882/08_2025/8j03_35882_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j03_35882/08_2025/8j03_35882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j03_35882/08_2025/8j03_35882.map" } resolution = 2.7 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= 0.003 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 S 88 5.16 5 C 9848 2.51 5 N 2576 2.21 5 O 2720 1.98 5 H 15084 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30316 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5427 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 6, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5427 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 6, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5427 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 6, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5427 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 6, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.46, per 1000 atoms: 0.18 Number of scatterers: 30316 At special positions: 0 Unit cell: (123.69, 122.76, 119.04, 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 88 16.00 O 2720 8.00 N 2576 7.00 C 9848 6.00 H 15084 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 684.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3512 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 4 sheets defined 82.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.533A pdb=" N TYR A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 114 removed outlier: 4.089A pdb=" N TYR A 95 " --> pdb=" O TRP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 3.790A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 155 through 165 Processing helix chain 'A' and resid 166 through 184 Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 255 Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 287 through 327 removed outlier: 3.987A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'A' and resid 332 through 348 removed outlier: 3.512A pdb=" N ALA A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 560 Processing helix chain 'A' and resid 564 through 595 removed outlier: 3.690A pdb=" N ILE A 568 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 91 through 114 removed outlier: 4.084A pdb=" N TYR D 95 " --> pdb=" O TRP D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 removed outlier: 3.795A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 155 through 165 Processing helix chain 'D' and resid 166 through 184 Processing helix chain 'D' and resid 196 through 210 Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 255 Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 287 through 327 removed outlier: 3.978A pdb=" N ILE D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 332 through 348 removed outlier: 3.544A pdb=" N ALA D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 560 Processing helix chain 'D' and resid 564 through 595 removed outlier: 3.694A pdb=" N ILE D 568 " --> pdb=" O VAL D 564 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 21 Processing helix chain 'E' and resid 29 through 41 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 65 through 75 Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'E' and resid 102 through 111 removed outlier: 3.922A pdb=" N THR E 111 " --> pdb=" O ARG E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 139 through 148 Processing helix chain 'G' and resid 71 through 86 Processing helix chain 'G' and resid 91 through 114 removed outlier: 4.084A pdb=" N TYR G 95 " --> pdb=" O TRP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 148 removed outlier: 3.795A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'G' and resid 155 through 165 Processing helix chain 'G' and resid 166 through 184 Processing helix chain 'G' and resid 196 through 210 Processing helix chain 'G' and resid 215 through 228 Processing helix chain 'G' and resid 228 through 255 Processing helix chain 'G' and resid 258 through 262 removed outlier: 3.835A pdb=" N ASP G 262 " --> pdb=" O ASP G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 276 Processing helix chain 'G' and resid 287 through 327 removed outlier: 3.979A pdb=" N ILE G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) Proline residue: G 308 - end of helix Processing helix chain 'G' and resid 332 through 348 removed outlier: 3.541A pdb=" N ALA G 336 " --> pdb=" O ARG G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 560 Processing helix chain 'G' and resid 564 through 595 removed outlier: 3.682A pdb=" N ILE G 568 " --> pdb=" O VAL G 564 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY G 594 " --> pdb=" O ASP G 590 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'H' and resid 102 through 111 removed outlier: 3.984A pdb=" N THR H 111 " --> pdb=" O ARG H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 139 through 148 Processing helix chain 'I' and resid 71 through 86 Processing helix chain 'I' and resid 91 through 114 removed outlier: 4.093A pdb=" N TYR I 95 " --> pdb=" O TRP I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 148 removed outlier: 3.796A pdb=" N ILE I 128 " --> pdb=" O GLY I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 151 No H-bonds generated for 'chain 'I' and resid 149 through 151' Processing helix chain 'I' and resid 155 through 165 Processing helix chain 'I' and resid 166 through 184 Processing helix chain 'I' and resid 196 through 210 Processing helix chain 'I' and resid 215 through 228 Processing helix chain 'I' and resid 228 through 255 Processing helix chain 'I' and resid 258 through 262 removed outlier: 3.835A pdb=" N ASP I 262 " --> pdb=" O ASP I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 263 through 276 Processing helix chain 'I' and resid 287 through 327 removed outlier: 3.925A pdb=" N ILE I 300 " --> pdb=" O THR I 296 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER I 303 " --> pdb=" O LEU I 299 " (cutoff:3.500A) Proline residue: I 308 - end of helix Processing helix chain 'I' and resid 332 through 348 removed outlier: 3.545A pdb=" N ALA I 336 " --> pdb=" O ARG I 332 " (cutoff:3.500A) Processing helix chain 'I' and resid 536 through 560 Processing helix chain 'I' and resid 564 through 595 removed outlier: 3.679A pdb=" N ILE I 568 " --> pdb=" O VAL I 564 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY I 594 " --> pdb=" O ASP I 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 21 Processing helix chain 'J' and resid 29 through 40 Processing helix chain 'J' and resid 45 through 57 Processing helix chain 'J' and resid 65 through 74 Processing helix chain 'J' and resid 82 through 94 Processing helix chain 'J' and resid 102 through 111 removed outlier: 3.877A pdb=" N THR J 111 " --> pdb=" O ARG J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 130 Processing helix chain 'J' and resid 139 through 148 Processing helix chain 'F' and resid 7 through 21 Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 102 through 111 removed outlier: 3.990A pdb=" N THR F 111 " --> pdb=" O ARG F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 139 through 148 Processing sheet with id=AA1, first strand: chain 'E' and resid 100 through 101 Processing sheet with id=AA2, first strand: chain 'H' and resid 100 through 101 Processing sheet with id=AA3, first strand: chain 'J' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'F' and resid 100 through 101 1166 hydrogen bonds defined for protein. 3480 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: 6.45 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15056 1.03 - 1.23: 50 1.23 - 1.42: 6630 1.42 - 1.62: 8736 1.62 - 1.81: 156 Bond restraints: 30628 Sorted by residual: bond pdb=" C07 P0T D 801 " pdb=" C09 P0T D 801 " ideal model delta sigma weight residual 1.336 1.594 -0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C07 P0T I 801 " pdb=" C09 P0T I 801 " ideal model delta sigma weight residual 1.336 1.594 -0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C07 P0T G 801 " pdb=" C09 P0T G 801 " ideal model delta sigma weight residual 1.336 1.594 -0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C07 P0T A 801 " pdb=" C09 P0T A 801 " ideal model delta sigma weight residual 1.336 1.594 -0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C10 P0T I 801 " pdb=" C19 P0T I 801 " ideal model delta sigma weight residual 1.331 1.550 -0.219 2.00e-02 2.50e+03 1.20e+02 ... (remaining 30623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.15: 55108 6.15 - 12.30: 4 12.30 - 18.45: 0 18.45 - 24.61: 4 24.61 - 30.76: 4 Bond angle restraints: 55120 Sorted by residual: angle pdb=" C07 P0T I 801 " pdb=" C04 P0T I 801 " pdb=" C08 P0T I 801 " ideal model delta sigma weight residual 112.03 81.27 30.76 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C07 P0T A 801 " pdb=" C04 P0T A 801 " pdb=" C08 P0T A 801 " ideal model delta sigma weight residual 112.03 81.28 30.75 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C07 P0T G 801 " pdb=" C04 P0T G 801 " pdb=" C08 P0T G 801 " ideal model delta sigma weight residual 112.03 81.32 30.71 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C07 P0T D 801 " pdb=" C04 P0T D 801 " pdb=" C08 P0T D 801 " ideal model delta sigma weight residual 112.03 81.33 30.70 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C03 P0T G 801 " pdb=" C04 P0T G 801 " pdb=" C08 P0T G 801 " ideal model delta sigma weight residual 111.12 130.77 -19.65 3.00e+00 1.11e-01 4.29e+01 ... (remaining 55115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 12740 21.25 - 42.51: 1128 42.51 - 63.76: 377 63.76 - 85.01: 35 85.01 - 106.27: 16 Dihedral angle restraints: 14296 sinusoidal: 7660 harmonic: 6636 Sorted by residual: dihedral pdb=" C03 P0T I 801 " pdb=" C05 P0T I 801 " pdb=" C06 P0T I 801 " pdb=" C09 P0T I 801 " ideal model delta sinusoidal sigma weight residual 49.00 -57.27 106.27 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" C03 P0T A 801 " pdb=" C05 P0T A 801 " pdb=" C06 P0T A 801 " pdb=" C09 P0T A 801 " ideal model delta sinusoidal sigma weight residual 49.00 -57.26 106.26 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" C03 P0T D 801 " pdb=" C05 P0T D 801 " pdb=" C06 P0T D 801 " pdb=" C09 P0T D 801 " ideal model delta sinusoidal sigma weight residual 49.00 -57.16 106.16 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 14293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1564 0.027 - 0.054: 455 0.054 - 0.080: 202 0.080 - 0.107: 73 0.107 - 0.134: 14 Chirality restraints: 2308 Sorted by residual: chirality pdb=" CB ILE D 134 " pdb=" CA ILE D 134 " pdb=" CG1 ILE D 134 " pdb=" CG2 ILE D 134 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CB ILE I 134 " pdb=" CA ILE I 134 " pdb=" CG1 ILE I 134 " pdb=" CG2 ILE I 134 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CB ILE G 134 " pdb=" CA ILE G 134 " pdb=" CG1 ILE G 134 " pdb=" CG2 ILE G 134 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 2305 not shown) Planarity restraints: 4480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 579 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C LEU D 579 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU D 579 " 0.011 2.00e-02 2.50e+03 pdb=" N SER D 580 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 579 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C LEU I 579 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU I 579 " -0.011 2.00e-02 2.50e+03 pdb=" N SER I 580 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 560 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO D 561 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 561 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 561 " 0.021 5.00e-02 4.00e+02 ... (remaining 4477 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1519 2.16 - 2.77: 59484 2.77 - 3.38: 89074 3.38 - 3.99: 106760 3.99 - 4.60: 168541 Nonbonded interactions: 425378 Sorted by model distance: nonbonded pdb=" OE1 GLU I 231 " pdb=" H GLU I 231 " model vdw 1.552 2.450 nonbonded pdb=" OE1 GLU G 231 " pdb=" H GLU G 231 " model vdw 1.552 2.450 nonbonded pdb="HE21 GLN I 341 " pdb=" O GLU J 115 " model vdw 1.582 2.450 nonbonded pdb="HE21 GLN D 341 " pdb=" O GLU E 115 " model vdw 1.583 2.450 nonbonded pdb="HE21 GLN G 341 " pdb=" O GLU H 115 " model vdw 1.585 2.450 ... (remaining 425373 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 0.200 Extract box with map and model: 0.300 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.920 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 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 : 0.008 0.258 15544 Z= 0.409 Angle : 0.754 30.757 20952 Z= 0.339 Chirality : 0.034 0.134 2308 Planarity : 0.004 0.040 2636 Dihedral : 18.805 106.267 5704 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.27 % Allowed : 29.29 % Favored : 68.43 % 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 aren not related in a simple way. whole: 1.00 (0.20), residues: 1860 helix: 1.01 (0.14), residues: 1468 sheet: None (None), residues: 0 loop : -0.39 (0.35), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 87 TYR 0.016 0.001 TYR A 127 PHE 0.010 0.001 PHE I 297 TRP 0.014 0.001 TRP I 344 HIS 0.003 0.001 HIS J 108 Details of bonding type rmsd covalent geometry : bond 0.00824 (15544) covalent geometry : angle 0.75438 (20952) hydrogen bonds : bond 0.12779 ( 1166) hydrogen bonds : angle 6.33635 ( 3480) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 163 PHE cc_start: 0.8389 (t80) cc_final: 0.8177 (t80) REVERT: D 211 MET cc_start: 0.8766 (tpp) cc_final: 0.8537 (ttt) REVERT: E 145 MET cc_start: 0.3327 (pp-130) cc_final: 0.2780 (tmm) REVERT: E 146 MET cc_start: 0.4532 (tpp) cc_final: 0.4087 (tpp) REVERT: G 229 SER cc_start: 0.8843 (t) cc_final: 0.8522 (p) REVERT: G 575 HIS cc_start: 0.7269 (OUTLIER) cc_final: 0.7027 (t-170) REVERT: I 226 TYR cc_start: 0.8535 (t80) cc_final: 0.8225 (t80) REVERT: I 229 SER cc_start: 0.8457 (t) cc_final: 0.8138 (p) REVERT: F 37 MET cc_start: 0.0731 (ttm) cc_final: 0.0498 (ttm) REVERT: F 77 MET cc_start: -0.0417 (mtt) cc_final: -0.0621 (mtt) REVERT: F 92 VAL cc_start: 0.6042 (t) cc_final: 0.5704 (t) REVERT: F 140 GLU cc_start: 0.7186 (mp0) cc_final: 0.6241 (tp30) REVERT: F 145 MET cc_start: 0.2536 (OUTLIER) cc_final: 0.2193 (tmm) outliers start: 36 outliers final: 17 residues processed: 223 average time/residue: 0.8505 time to fit residues: 216.1971 Evaluate side-chains 180 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 262 ASP Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 575 HIS Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 262 ASP Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.5980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.226759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.139570 restraints weight = 61720.351| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 5.56 r_work: 0.3372 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15544 Z= 0.183 Angle : 0.556 6.672 20952 Z= 0.298 Chirality : 0.035 0.151 2308 Planarity : 0.004 0.035 2636 Dihedral : 8.673 57.995 2191 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.22 % Allowed : 28.09 % Favored : 68.69 % 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 aren not related in a simple way. whole: 1.82 (0.20), residues: 1860 helix: 1.63 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.38 (0.35), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 333 TYR 0.010 0.001 TYR I 571 PHE 0.010 0.001 PHE A 240 TRP 0.016 0.001 TRP G 344 HIS 0.002 0.001 HIS J 108 Details of bonding type rmsd covalent geometry : bond 0.00393 (15544) covalent geometry : angle 0.55635 (20952) hydrogen bonds : bond 0.04685 ( 1166) hydrogen bonds : angle 4.82414 ( 3480) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.2168 (mmt) cc_final: 0.1918 (mtp) REVERT: D 163 PHE cc_start: 0.8339 (t80) cc_final: 0.8100 (t80) REVERT: D 211 MET cc_start: 0.8793 (tpp) cc_final: 0.8580 (ttt) REVERT: E 145 MET cc_start: 0.3166 (OUTLIER) cc_final: 0.2726 (tmm) REVERT: I 117 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8000 (mp0) REVERT: F 77 MET cc_start: -0.0470 (mtt) cc_final: -0.0670 (mtt) REVERT: F 145 MET cc_start: 0.2699 (OUTLIER) cc_final: 0.2499 (tmm) outliers start: 51 outliers final: 21 residues processed: 194 average time/residue: 0.7244 time to fit residues: 163.1482 Evaluate side-chains 180 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 187 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.226013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.138364 restraints weight = 61774.268| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 5.34 r_work: 0.3356 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15544 Z= 0.179 Angle : 0.530 6.835 20952 Z= 0.286 Chirality : 0.035 0.142 2308 Planarity : 0.004 0.038 2636 Dihedral : 7.302 53.718 2180 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.98 % Allowed : 26.77 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.20), residues: 1860 helix: 1.76 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -0.69 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 87 TYR 0.008 0.001 TYR A 571 PHE 0.010 0.001 PHE G 346 TRP 0.016 0.001 TRP I 344 HIS 0.004 0.001 HIS D 575 Details of bonding type rmsd covalent geometry : bond 0.00390 (15544) covalent geometry : angle 0.52996 (20952) hydrogen bonds : bond 0.04216 ( 1166) hydrogen bonds : angle 4.52549 ( 3480) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 234 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 171 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.2564 (mmt) cc_final: 0.2260 (mtp) REVERT: D 163 PHE cc_start: 0.8306 (t80) cc_final: 0.8035 (t80) REVERT: E 145 MET cc_start: 0.3006 (OUTLIER) cc_final: 0.2607 (tmm) REVERT: E 146 MET cc_start: 0.4504 (tpp) cc_final: 0.4299 (tpp) REVERT: I 117 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8018 (mp0) REVERT: I 134 ILE cc_start: 0.8114 (pp) cc_final: 0.7886 (pp) REVERT: F 52 MET cc_start: -0.4229 (mtm) cc_final: -0.4485 (mtm) REVERT: F 145 MET cc_start: 0.3025 (OUTLIER) cc_final: 0.2725 (tmm) outliers start: 63 outliers final: 25 residues processed: 211 average time/residue: 0.7459 time to fit residues: 183.4405 Evaluate side-chains 180 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 168 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 161 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.226084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.138818 restraints weight = 61324.580| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 5.38 r_work: 0.3371 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15544 Z= 0.151 Angle : 0.502 5.684 20952 Z= 0.271 Chirality : 0.034 0.137 2308 Planarity : 0.003 0.036 2636 Dihedral : 6.825 56.666 2176 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.28 % Allowed : 26.89 % Favored : 69.82 % 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 aren not related in a simple way. whole: 2.03 (0.20), residues: 1860 helix: 1.86 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.68 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.009 0.001 TYR A 571 PHE 0.009 0.001 PHE G 329 TRP 0.016 0.001 TRP A 344 HIS 0.003 0.001 HIS I 575 Details of bonding type rmsd covalent geometry : bond 0.00326 (15544) covalent geometry : angle 0.50165 (20952) hydrogen bonds : bond 0.03912 ( 1166) hydrogen bonds : angle 4.37435 ( 3480) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.2711 (mmt) cc_final: 0.2454 (mtp) REVERT: D 163 PHE cc_start: 0.8302 (t80) cc_final: 0.8030 (t80) REVERT: E 37 MET cc_start: 0.0380 (OUTLIER) cc_final: -0.0046 (tmm) REVERT: E 145 MET cc_start: 0.3106 (OUTLIER) cc_final: 0.2821 (tmm) REVERT: H 146 MET cc_start: 0.3796 (tpp) cc_final: 0.3593 (tpp) REVERT: I 117 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7936 (mp0) REVERT: F 145 MET cc_start: 0.3114 (OUTLIER) cc_final: 0.2815 (tmm) outliers start: 52 outliers final: 25 residues processed: 198 average time/residue: 0.7325 time to fit residues: 166.7490 Evaluate side-chains 178 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 552 LYS Chi-restraints excluded: chain I residue 575 HIS Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 70 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 ASN E 42 GLN E 98 ASN H 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.226942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.141544 restraints weight = 61876.364| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 5.30 r_work: 0.3394 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15544 Z= 0.121 Angle : 0.487 6.084 20952 Z= 0.262 Chirality : 0.033 0.126 2308 Planarity : 0.003 0.040 2636 Dihedral : 6.118 58.816 2176 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.65 % Allowed : 27.59 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.20), residues: 1860 helix: 2.02 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.72 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.009 0.001 TYR A 571 PHE 0.009 0.001 PHE G 329 TRP 0.016 0.001 TRP I 344 HIS 0.002 0.001 HIS G 96 Details of bonding type rmsd covalent geometry : bond 0.00260 (15544) covalent geometry : angle 0.48726 (20952) hydrogen bonds : bond 0.03716 ( 1166) hydrogen bonds : angle 4.24519 ( 3480) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.2670 (mmt) cc_final: 0.2462 (mtp) REVERT: D 163 PHE cc_start: 0.8270 (t80) cc_final: 0.8002 (t80) REVERT: E 145 MET cc_start: 0.3172 (OUTLIER) cc_final: 0.2732 (tmm) REVERT: H 146 MET cc_start: 0.3699 (tpp) cc_final: 0.3458 (tpp) REVERT: F 145 MET cc_start: 0.2907 (OUTLIER) cc_final: 0.2624 (tmm) outliers start: 42 outliers final: 25 residues processed: 184 average time/residue: 0.9953 time to fit residues: 210.3657 Evaluate side-chains 171 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 552 LYS Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 75 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 166 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 55 optimal weight: 0.1980 chunk 112 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.226390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.139667 restraints weight = 61691.673| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 5.42 r_work: 0.3374 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15544 Z= 0.142 Angle : 0.493 6.508 20952 Z= 0.266 Chirality : 0.033 0.130 2308 Planarity : 0.003 0.036 2636 Dihedral : 6.115 59.681 2176 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.65 % Allowed : 27.84 % Favored : 69.51 % 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 aren not related in a simple way. whole: 2.24 (0.20), residues: 1860 helix: 2.04 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.73 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 87 TYR 0.009 0.001 TYR A 571 PHE 0.009 0.001 PHE G 329 TRP 0.015 0.001 TRP I 344 HIS 0.002 0.001 HIS J 108 Details of bonding type rmsd covalent geometry : bond 0.00309 (15544) covalent geometry : angle 0.49304 (20952) hydrogen bonds : bond 0.03706 ( 1166) hydrogen bonds : angle 4.22527 ( 3480) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.2772 (mmt) cc_final: 0.2556 (mtp) REVERT: D 79 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7941 (p0) REVERT: D 163 PHE cc_start: 0.8278 (t80) cc_final: 0.8002 (t80) REVERT: D 557 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7590 (pp20) REVERT: E 145 MET cc_start: 0.3123 (OUTLIER) cc_final: 0.2759 (tmm) REVERT: H 145 MET cc_start: 0.2266 (OUTLIER) cc_final: 0.1834 (tmm) REVERT: H 146 MET cc_start: 0.3598 (tpp) cc_final: 0.3297 (tpp) REVERT: F 145 MET cc_start: 0.2954 (OUTLIER) cc_final: 0.2685 (tmm) outliers start: 42 outliers final: 24 residues processed: 172 average time/residue: 0.9986 time to fit residues: 196.4207 Evaluate side-chains 172 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 552 LYS Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 4 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 168 optimal weight: 20.0000 chunk 50 optimal weight: 0.0470 chunk 138 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.226254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.141167 restraints weight = 61484.202| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 5.80 r_work: 0.3368 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15544 Z= 0.141 Angle : 0.494 7.575 20952 Z= 0.267 Chirality : 0.033 0.129 2308 Planarity : 0.003 0.037 2636 Dihedral : 6.001 57.954 2176 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.53 % Allowed : 27.71 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.20), residues: 1860 helix: 2.08 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.73 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 87 TYR 0.009 0.001 TYR A 571 PHE 0.009 0.001 PHE G 329 TRP 0.016 0.001 TRP I 344 HIS 0.002 0.001 HIS J 108 Details of bonding type rmsd covalent geometry : bond 0.00308 (15544) covalent geometry : angle 0.49439 (20952) hydrogen bonds : bond 0.03660 ( 1166) hydrogen bonds : angle 4.19925 ( 3480) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.2815 (mmt) cc_final: 0.2566 (mtp) REVERT: D 163 PHE cc_start: 0.8277 (t80) cc_final: 0.7997 (t80) REVERT: D 557 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7562 (pp20) REVERT: E 145 MET cc_start: 0.3157 (OUTLIER) cc_final: 0.2822 (tmm) REVERT: G 546 MET cc_start: 0.3387 (mpm) cc_final: 0.2996 (mtp) REVERT: H 146 MET cc_start: 0.3698 (tpp) cc_final: 0.3455 (tpp) REVERT: J 145 MET cc_start: 0.2053 (OUTLIER) cc_final: 0.1654 (tmm) REVERT: F 145 MET cc_start: 0.3120 (OUTLIER) cc_final: 0.2879 (tmm) outliers start: 40 outliers final: 25 residues processed: 178 average time/residue: 0.8990 time to fit residues: 184.2886 Evaluate side-chains 175 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 552 LYS Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 41 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 180 optimal weight: 30.0000 chunk 37 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.223187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.132584 restraints weight = 61475.324| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 4.03 r_work: 0.3339 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15544 Z= 0.286 Angle : 0.569 7.089 20952 Z= 0.313 Chirality : 0.039 0.159 2308 Planarity : 0.004 0.037 2636 Dihedral : 7.451 56.163 2176 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.97 % Allowed : 27.27 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.20), residues: 1860 helix: 1.70 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.78 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 87 TYR 0.010 0.001 TYR D 571 PHE 0.012 0.002 PHE I 329 TRP 0.022 0.002 TRP D 344 HIS 0.006 0.001 HIS I 575 Details of bonding type rmsd covalent geometry : bond 0.00636 (15544) covalent geometry : angle 0.56906 (20952) hydrogen bonds : bond 0.04147 ( 1166) hydrogen bonds : angle 4.44874 ( 3480) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.2831 (mmt) cc_final: 0.2582 (mtp) REVERT: D 557 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7603 (pp20) REVERT: E 145 MET cc_start: 0.3361 (OUTLIER) cc_final: 0.3067 (tmm) REVERT: G 546 MET cc_start: 0.3462 (OUTLIER) cc_final: 0.3034 (mtp) REVERT: G 557 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7678 (pp20) REVERT: J 87 ARG cc_start: 0.5657 (mmp80) cc_final: 0.5453 (mmp80) REVERT: J 145 MET cc_start: 0.2571 (OUTLIER) cc_final: 0.2226 (tmm) REVERT: F 73 MET cc_start: 0.0777 (pmm) cc_final: -0.0082 (mmm) outliers start: 47 outliers final: 27 residues processed: 182 average time/residue: 0.8789 time to fit residues: 181.9218 Evaluate side-chains 180 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 557 GLU Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 552 LYS Chi-restraints excluded: chain I residue 575 HIS Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 8 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 183 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.225048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.135391 restraints weight = 61650.825| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 4.04 r_work: 0.3383 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15544 Z= 0.170 Angle : 0.527 8.974 20952 Z= 0.285 Chirality : 0.034 0.134 2308 Planarity : 0.004 0.039 2636 Dihedral : 6.632 56.153 2173 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.59 % Allowed : 27.53 % Favored : 69.89 % 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 aren not related in a simple way. whole: 1.90 (0.20), residues: 1860 helix: 1.78 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.79 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 87 TYR 0.012 0.001 TYR G 127 PHE 0.010 0.001 PHE G 329 TRP 0.017 0.001 TRP D 344 HIS 0.003 0.001 HIS J 108 Details of bonding type rmsd covalent geometry : bond 0.00371 (15544) covalent geometry : angle 0.52691 (20952) hydrogen bonds : bond 0.03843 ( 1166) hydrogen bonds : angle 4.31800 ( 3480) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 557 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7538 (pp20) REVERT: E 145 MET cc_start: 0.3572 (OUTLIER) cc_final: 0.3286 (tmm) REVERT: G 546 MET cc_start: 0.3480 (OUTLIER) cc_final: 0.3037 (mtp) REVERT: G 557 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7672 (pp20) REVERT: J 145 MET cc_start: 0.2557 (OUTLIER) cc_final: 0.2218 (tmm) REVERT: F 73 MET cc_start: 0.0968 (pmm) cc_final: 0.0040 (mmm) outliers start: 41 outliers final: 29 residues processed: 173 average time/residue: 0.8676 time to fit residues: 170.7273 Evaluate side-chains 184 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 557 GLU Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 552 LYS Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 13 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 22 optimal weight: 0.2980 chunk 25 optimal weight: 9.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.223621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.133503 restraints weight = 61065.430| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 4.02 r_work: 0.3353 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15544 Z= 0.249 Angle : 0.566 7.921 20952 Z= 0.309 Chirality : 0.037 0.146 2308 Planarity : 0.004 0.049 2636 Dihedral : 6.668 55.984 2173 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.34 % Allowed : 27.97 % Favored : 69.70 % 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 aren not related in a simple way. whole: 1.72 (0.20), residues: 1860 helix: 1.65 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.83 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG J 87 TYR 0.011 0.001 TYR G 127 PHE 0.013 0.001 PHE J 69 TRP 0.023 0.002 TRP D 344 HIS 0.005 0.001 HIS J 108 Details of bonding type rmsd covalent geometry : bond 0.00551 (15544) covalent geometry : angle 0.56632 (20952) hydrogen bonds : bond 0.04058 ( 1166) hydrogen bonds : angle 4.44292 ( 3480) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 557 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7560 (pp20) REVERT: E 145 MET cc_start: 0.3729 (OUTLIER) cc_final: 0.3468 (tmm) REVERT: G 546 MET cc_start: 0.3441 (OUTLIER) cc_final: 0.2981 (mtp) REVERT: G 557 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7702 (pp20) REVERT: J 73 MET cc_start: 0.1776 (pmm) cc_final: 0.0137 (ttm) REVERT: J 145 MET cc_start: 0.2786 (OUTLIER) cc_final: 0.2491 (tmm) REVERT: F 73 MET cc_start: 0.1008 (pmm) cc_final: 0.0035 (mmm) outliers start: 37 outliers final: 28 residues processed: 168 average time/residue: 1.0849 time to fit residues: 206.7186 Evaluate side-chains 179 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 557 GLU Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain I residue 552 LYS Chi-restraints excluded: chain I residue 581 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 41 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 181 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 161 optimal weight: 20.0000 chunk 131 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.225985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.139408 restraints weight = 61383.994| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 5.18 r_work: 0.3376 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15544 Z= 0.136 Angle : 0.520 8.429 20952 Z= 0.280 Chirality : 0.034 0.139 2308 Planarity : 0.004 0.049 2636 Dihedral : 6.045 56.610 2173 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.27 % Allowed : 28.16 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.20), residues: 1860 helix: 1.84 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.77 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG J 87 TYR 0.011 0.001 TYR G 127 PHE 0.011 0.001 PHE D 163 TRP 0.017 0.001 TRP D 344 HIS 0.002 0.001 HIS J 108 Details of bonding type rmsd covalent geometry : bond 0.00294 (15544) covalent geometry : angle 0.51964 (20952) hydrogen bonds : bond 0.03694 ( 1166) hydrogen bonds : angle 4.27044 ( 3480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14685.46 seconds wall clock time: 248 minutes 20.52 seconds (14900.52 seconds total)