Starting phenix.real_space_refine on Thu Jun 26 03:28:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j03_35882/06_2025/8j03_35882_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j03_35882/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j03_35882/06_2025/8j03_35882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j03_35882/06_2025/8j03_35882.map" model { file = "/net/cci-nas-00/data/ceres_data/8j03_35882/06_2025/8j03_35882_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j03_35882/06_2025/8j03_35882_neut_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.83, per 1000 atoms: 0.56 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: 9.88 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 2.59 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: 11.47 Time building geometry restraints manager: 10.54 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: 0.03 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.530 Extract box with map and model: 1.230 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 70.830 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.150 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:59.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.870 ------------------------------------------------------------------------------- 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 : 12.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (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 TRP 0.014 0.001 TRP I 344 HIS 0.003 0.001 HIS J 108 PHE 0.010 0.001 PHE I 297 TYR 0.016 0.001 TYR A 127 ARG 0.005 0.000 ARG F 87 Details of bonding type rmsd hydrogen bonds : bond 0.12779 ( 1166) hydrogen bonds : angle 6.33635 ( 3480) covalent geometry : bond 0.00824 (15544) covalent geometry : angle 0.75438 (20952) *********************** 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 : 2.811 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: 2.1714 time to fit residues: 560.0739 Evaluate side-chains 179 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 2.452 ------------------------------------------------------------------------------- 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 158 optimal weight: 20.0000 chunk 142 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 147 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 170 optimal weight: 0.3980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.228098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.143129 restraints weight = 61703.701| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 5.03 r_work: 0.3436 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15544 Z= 0.137 Angle : 0.534 5.507 20952 Z= 0.285 Chirality : 0.034 0.140 2308 Planarity : 0.004 0.034 2636 Dihedral : 8.392 54.484 2191 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.71 % Allowed : 28.28 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.20), residues: 1860 helix: 1.73 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.32 (0.35), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 344 HIS 0.002 0.001 HIS I 575 PHE 0.010 0.001 PHE G 346 TYR 0.010 0.001 TYR I 571 ARG 0.006 0.000 ARG I 201 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 1166) hydrogen bonds : angle 4.70148 ( 3480) covalent geometry : bond 0.00284 (15544) covalent geometry : angle 0.53423 (20952) *********************** 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 219 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 2.758 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: 0.2323 (mmt) cc_final: 0.2033 (mtp) REVERT: D 163 PHE cc_start: 0.8341 (t80) cc_final: 0.8096 (t80) REVERT: E 145 MET cc_start: 0.3315 (OUTLIER) cc_final: 0.2842 (tmm) REVERT: I 117 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7993 (mp0) REVERT: I 229 SER cc_start: 0.8861 (t) cc_final: 0.8639 (p) REVERT: F 140 GLU cc_start: 0.6910 (mp0) cc_final: 0.6228 (tp30) REVERT: F 145 MET cc_start: 0.2649 (pp-130) cc_final: 0.2423 (tmm) outliers start: 43 outliers final: 16 residues processed: 199 average time/residue: 1.8025 time to fit residues: 416.4252 Evaluate side-chains 177 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 2.441 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.227206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.139955 restraints weight = 61778.836| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 5.49 r_work: 0.3387 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15544 Z= 0.146 Angle : 0.504 6.628 20952 Z= 0.272 Chirality : 0.034 0.134 2308 Planarity : 0.003 0.036 2636 Dihedral : 6.496 53.292 2173 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.91 % Allowed : 25.88 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.20), residues: 1860 helix: 1.91 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : -0.64 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 344 HIS 0.003 0.001 HIS D 575 PHE 0.009 0.001 PHE D 329 TYR 0.010 0.001 TYR I 237 ARG 0.011 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 1166) hydrogen bonds : angle 4.42271 ( 3480) covalent geometry : bond 0.00314 (15544) covalent geometry : angle 0.50406 (20952) *********************** 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 229 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 167 time to evaluate : 2.511 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: A 226 TYR cc_start: 0.9194 (t80) cc_final: 0.8990 (t80) REVERT: A 546 MET cc_start: 0.2501 (mmt) cc_final: 0.2199 (mtp) REVERT: D 163 PHE cc_start: 0.8294 (t80) cc_final: 0.8042 (t80) REVERT: D 211 MET cc_start: 0.8790 (tpp) cc_final: 0.8556 (ttt) REVERT: D 578 MET cc_start: 0.6928 (tmm) cc_final: 0.5579 (tpp) REVERT: E 145 MET cc_start: 0.3071 (OUTLIER) cc_final: 0.2641 (tmm) REVERT: I 117 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8008 (mp0) REVERT: I 134 ILE cc_start: 0.8026 (pp) cc_final: 0.7764 (pp) REVERT: F 145 MET cc_start: 0.3025 (OUTLIER) cc_final: 0.2706 (tmm) outliers start: 62 outliers final: 24 residues processed: 208 average time/residue: 1.9236 time to fit residues: 477.6296 Evaluate side-chains 182 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 2.533 ------------------------------------------------------------------------------- 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 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 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 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 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 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 186 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.225859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.138726 restraints weight = 61913.635| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 5.51 r_work: 0.3359 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15544 Z= 0.175 Angle : 0.509 5.480 20952 Z= 0.276 Chirality : 0.034 0.141 2308 Planarity : 0.003 0.034 2636 Dihedral : 6.861 57.565 2173 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.71 % Allowed : 27.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.20), residues: 1860 helix: 1.93 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.77 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 344 HIS 0.004 0.001 HIS A 575 PHE 0.010 0.001 PHE G 329 TYR 0.010 0.001 TYR D 571 ARG 0.007 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 1166) hydrogen bonds : angle 4.34401 ( 3480) covalent geometry : bond 0.00385 (15544) covalent geometry : angle 0.50859 (20952) *********************** 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 206 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 2.605 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: A 546 MET cc_start: 0.2688 (mmt) cc_final: 0.2481 (mtp) REVERT: D 163 PHE cc_start: 0.8249 (t80) cc_final: 0.8009 (t80) REVERT: D 211 MET cc_start: 0.8838 (tpp) cc_final: 0.8582 (ttt) REVERT: E 145 MET cc_start: 0.3084 (OUTLIER) cc_final: 0.2790 (tmm) REVERT: H 146 MET cc_start: 0.3691 (tpp) cc_final: 0.3462 (tpp) REVERT: I 117 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7934 (mp0) REVERT: F 145 MET cc_start: 0.2983 (OUTLIER) cc_final: 0.2689 (tmm) outliers start: 43 outliers final: 24 residues processed: 189 average time/residue: 2.1629 time to fit residues: 492.3005 Evaluate side-chains 175 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 2.799 ------------------------------------------------------------------------------- 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 A residue 575 HIS 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 229 SER 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 145 ILE 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 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 115 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 69 optimal weight: 30.0000 chunk 123 optimal weight: 30.0000 chunk 54 optimal weight: 2.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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** D 79 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.224730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.136801 restraints weight = 61560.400| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 5.25 r_work: 0.3369 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15544 Z= 0.210 Angle : 0.527 6.233 20952 Z= 0.287 Chirality : 0.036 0.147 2308 Planarity : 0.004 0.039 2636 Dihedral : 7.201 59.899 2173 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.85 % Allowed : 26.77 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.20), residues: 1860 helix: 1.83 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.74 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 344 HIS 0.005 0.001 HIS A 575 PHE 0.011 0.001 PHE G 329 TYR 0.008 0.001 TYR G 571 ARG 0.006 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 1166) hydrogen bonds : angle 4.37715 ( 3480) covalent geometry : bond 0.00461 (15544) covalent geometry : angle 0.52727 (20952) *********************** 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 213 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 152 time to evaluate : 2.313 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: 0.2731 (mmt) cc_final: 0.2480 (mtp) REVERT: D 557 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7529 (pp20) REVERT: E 37 MET cc_start: 0.0583 (OUTLIER) cc_final: 0.0072 (tmm) REVERT: E 145 MET cc_start: 0.3257 (OUTLIER) cc_final: 0.2823 (tmm) REVERT: G 546 MET cc_start: 0.2585 (mpt) cc_final: 0.2063 (mtp) REVERT: G 557 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7690 (pp20) REVERT: H 146 MET cc_start: 0.3812 (tpp) cc_final: 0.3586 (tpp) REVERT: F 145 MET cc_start: 0.3247 (OUTLIER) cc_final: 0.2988 (tmm) outliers start: 61 outliers final: 27 residues processed: 197 average time/residue: 2.0230 time to fit residues: 460.6298 Evaluate side-chains 178 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 2.493 ------------------------------------------------------------------------------- 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 176 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain D residue 77 LEU 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 37 MET 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 557 GLU Chi-restraints excluded: chain G residue 575 HIS 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 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 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 129 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 179 optimal weight: 40.0000 chunk 115 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 155 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 42 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.225405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.138183 restraints weight = 61484.504| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 5.24 r_work: 0.3359 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15544 Z= 0.164 Angle : 0.506 6.507 20952 Z= 0.275 Chirality : 0.034 0.135 2308 Planarity : 0.004 0.045 2636 Dihedral : 6.737 58.529 2173 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.09 % Allowed : 27.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.20), residues: 1860 helix: 1.89 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.71 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 344 HIS 0.004 0.001 HIS A 575 PHE 0.010 0.001 PHE G 329 TYR 0.009 0.001 TYR D 571 ARG 0.011 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 1166) hydrogen bonds : angle 4.29715 ( 3480) covalent geometry : bond 0.00360 (15544) covalent geometry : angle 0.50626 (20952) *********************** 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 204 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.2802 (mmt) cc_final: 0.2548 (mtp) REVERT: D 211 MET cc_start: 0.8920 (tpp) cc_final: 0.8668 (ttt) REVERT: D 557 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7559 (pp20) REVERT: E 145 MET cc_start: 0.3210 (OUTLIER) cc_final: 0.2884 (tmm) REVERT: G 546 MET cc_start: 0.2512 (mpt) cc_final: 0.1992 (mtp) REVERT: H 146 MET cc_start: 0.3883 (tpp) cc_final: 0.3672 (tpp) REVERT: F 145 MET cc_start: 0.3011 (OUTLIER) cc_final: 0.2753 (tmm) outliers start: 49 outliers final: 29 residues processed: 185 average time/residue: 2.0284 time to fit residues: 435.9664 Evaluate side-chains 181 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 2.725 ------------------------------------------------------------------------------- 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 176 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 575 HIS 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 557 GLU Chi-restraints excluded: chain D residue 575 HIS 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 229 SER Chi-restraints excluded: chain G residue 575 HIS 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 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 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 151 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 150 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 ** 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 = 0.4781 r_free = 0.4781 target = 0.225658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.137579 restraints weight = 61342.269| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 4.65 r_work: 0.3388 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15544 Z= 0.148 Angle : 0.507 6.886 20952 Z= 0.274 Chirality : 0.034 0.131 2308 Planarity : 0.003 0.039 2636 Dihedral : 6.349 58.996 2173 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.65 % Allowed : 27.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.20), residues: 1860 helix: 1.92 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.69 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 344 HIS 0.003 0.001 HIS J 108 PHE 0.009 0.001 PHE G 329 TYR 0.009 0.001 TYR D 571 ARG 0.008 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 1166) hydrogen bonds : angle 4.26569 ( 3480) covalent geometry : bond 0.00321 (15544) covalent geometry : angle 0.50652 (20952) *********************** 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 199 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 2.837 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: A 546 MET cc_start: 0.2838 (mmt) cc_final: 0.2597 (mtp) REVERT: D 211 MET cc_start: 0.8885 (tpp) cc_final: 0.8641 (ttt) REVERT: D 557 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7602 (pp20) REVERT: E 145 MET cc_start: 0.3312 (OUTLIER) cc_final: 0.2997 (tmm) REVERT: G 546 MET cc_start: 0.2536 (mpt) cc_final: 0.2016 (mtp) REVERT: G 557 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7710 (pp20) REVERT: F 73 MET cc_start: 0.0587 (pmm) cc_final: -0.0263 (mmm) REVERT: F 145 MET cc_start: 0.3236 (OUTLIER) cc_final: 0.2990 (tmm) outliers start: 42 outliers final: 27 residues processed: 184 average time/residue: 1.9564 time to fit residues: 417.8439 Evaluate side-chains 180 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 2.461 ------------------------------------------------------------------------------- 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 176 LEU Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 575 HIS 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 229 SER Chi-restraints excluded: chain G residue 557 GLU Chi-restraints excluded: chain G residue 575 HIS 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 145 ILE 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 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 52 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 77 optimal weight: 0.3980 chunk 176 optimal weight: 20.0000 chunk 185 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 137 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 overall best weight: 1.9982 ------------------------------------------------------------------------------- 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 = 0.4782 r_free = 0.4782 target = 0.225669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.137254 restraints weight = 61327.273| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 4.97 r_work: 0.3380 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15544 Z= 0.150 Angle : 0.505 7.099 20952 Z= 0.273 Chirality : 0.034 0.151 2308 Planarity : 0.003 0.038 2636 Dihedral : 6.087 58.168 2173 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.53 % Allowed : 27.84 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.20), residues: 1860 helix: 1.96 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.72 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 344 HIS 0.003 0.001 HIS D 575 PHE 0.010 0.001 PHE J 20 TYR 0.013 0.001 TYR G 127 ARG 0.008 0.000 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 1166) hydrogen bonds : angle 4.23573 ( 3480) covalent geometry : bond 0.00326 (15544) covalent geometry : angle 0.50450 (20952) *********************** 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 192 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 2.981 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: 0.2796 (mmt) cc_final: 0.2567 (mtp) REVERT: D 557 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7604 (pp20) REVERT: E 145 MET cc_start: 0.3406 (OUTLIER) cc_final: 0.3073 (tmm) REVERT: G 546 MET cc_start: 0.2669 (mpt) cc_final: 0.2151 (mtp) REVERT: G 557 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7760 (pp20) REVERT: F 73 MET cc_start: 0.0881 (OUTLIER) cc_final: 0.0016 (mmm) outliers start: 40 outliers final: 29 residues processed: 178 average time/residue: 2.5643 time to fit residues: 531.3168 Evaluate side-chains 182 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 3.891 ------------------------------------------------------------------------------- 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 A residue 346 PHE Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain D residue 77 LEU 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 229 SER Chi-restraints excluded: chain G residue 557 GLU Chi-restraints excluded: chain G residue 575 HIS 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 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 F residue 73 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 133 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.4786 r_free = 0.4786 target = 0.226258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.139478 restraints weight = 61361.799| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 5.56 r_work: 0.3372 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15544 Z= 0.139 Angle : 0.507 9.157 20952 Z= 0.273 Chirality : 0.034 0.131 2308 Planarity : 0.003 0.051 2636 Dihedral : 5.862 57.374 2173 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.34 % Allowed : 28.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.20), residues: 1860 helix: 1.99 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.67 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 344 HIS 0.002 0.001 HIS A 575 PHE 0.010 0.001 PHE A 346 TYR 0.009 0.001 TYR G 127 ARG 0.011 0.000 ARG J 87 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 1166) hydrogen bonds : angle 4.21211 ( 3480) covalent geometry : bond 0.00302 (15544) covalent geometry : angle 0.50736 (20952) *********************** 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 189 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.2800 (mmt) cc_final: 0.2565 (mtp) REVERT: D 211 MET cc_start: 0.8915 (tpp) cc_final: 0.8674 (ttt) REVERT: D 557 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7614 (pp20) REVERT: E 145 MET cc_start: 0.3257 (OUTLIER) cc_final: 0.2911 (tmm) REVERT: G 546 MET cc_start: 0.2655 (mpt) cc_final: 0.2103 (mtp) REVERT: G 557 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7759 (pp20) REVERT: J 73 MET cc_start: 0.1725 (pmm) cc_final: 0.0213 (ttm) REVERT: F 73 MET cc_start: 0.0783 (OUTLIER) cc_final: -0.0103 (mmm) outliers start: 37 outliers final: 27 residues processed: 175 average time/residue: 1.9528 time to fit residues: 393.0365 Evaluate side-chains 176 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 2.519 ------------------------------------------------------------------------------- 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 A residue 346 PHE Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain D residue 77 LEU 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 557 GLU Chi-restraints excluded: chain G residue 575 HIS 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 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 F residue 73 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 108 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 156 optimal weight: 20.0000 chunk 149 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 170 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 = 0.4776 r_free = 0.4776 target = 0.224838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.135771 restraints weight = 61522.598| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 4.84 r_work: 0.3363 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15544 Z= 0.191 Angle : 0.531 7.135 20952 Z= 0.287 Chirality : 0.035 0.140 2308 Planarity : 0.004 0.040 2636 Dihedral : 6.136 57.326 2173 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.27 % Allowed : 28.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.20), residues: 1860 helix: 1.88 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.72 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 344 HIS 0.005 0.001 HIS D 575 PHE 0.010 0.001 PHE G 329 TYR 0.009 0.001 TYR G 127 ARG 0.010 0.000 ARG E 38 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 1166) hydrogen bonds : angle 4.28862 ( 3480) covalent geometry : bond 0.00422 (15544) covalent geometry : angle 0.53083 (20952) ********************** 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 187 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.2835 (mmt) cc_final: 0.2594 (mtp) REVERT: D 211 MET cc_start: 0.8870 (tpp) cc_final: 0.8648 (ttt) REVERT: D 557 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7601 (pp20) REVERT: E 145 MET cc_start: 0.3414 (OUTLIER) cc_final: 0.3089 (tmm) REVERT: G 546 MET cc_start: 0.2687 (mpt) cc_final: 0.2117 (mtp) REVERT: G 557 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7797 (pp20) REVERT: H 87 ARG cc_start: 0.5525 (mmp80) cc_final: 0.5079 (mmp80) REVERT: J 73 MET cc_start: 0.1583 (pmm) cc_final: 0.0055 (ttm) REVERT: F 73 MET cc_start: 0.0926 (OUTLIER) cc_final: -0.0052 (mmm) outliers start: 36 outliers final: 27 residues processed: 174 average time/residue: 2.4570 time to fit residues: 493.6499 Evaluate side-chains 180 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 5.281 ------------------------------------------------------------------------------- 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 A residue 346 PHE Chi-restraints excluded: chain A residue 575 HIS Chi-restraints excluded: chain D residue 77 LEU 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 557 GLU Chi-restraints excluded: chain G residue 575 HIS 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 581 ARG Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain F residue 73 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 99 optimal weight: 0.1980 chunk 162 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 177 optimal weight: 0.3980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** ** I 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.226799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.137862 restraints weight = 61132.340| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.86 r_work: 0.3407 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3223 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= 0.118 Angle : 0.507 7.892 20952 Z= 0.271 Chirality : 0.033 0.126 2308 Planarity : 0.004 0.057 2636 Dihedral : 5.729 57.129 2173 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.96 % Allowed : 28.72 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.20), residues: 1860 helix: 2.03 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.68 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 344 HIS 0.002 0.001 HIS A 575 PHE 0.010 0.001 PHE A 346 TYR 0.009 0.001 TYR G 127 ARG 0.020 0.000 ARG J 87 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 1166) hydrogen bonds : angle 4.17329 ( 3480) covalent geometry : bond 0.00254 (15544) covalent geometry : angle 0.50688 (20952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31822.22 seconds wall clock time: 557 minutes 19.86 seconds (33439.86 seconds total)