Starting phenix.real_space_refine on Thu Aug 6 10:01:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gpn_34195/08_2026/8gpn_34195.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gpn_34195/08_2026/8gpn_34195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gpn_34195/08_2026/8gpn_34195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gpn_34195/08_2026/8gpn_34195.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gpn_34195/08_2026/8gpn_34195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gpn_34195/08_2026/8gpn_34195.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8gpn_34195/08_2026/8gpn_34195.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gpn_34195/08_2026/8gpn_34195.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 27 5.16 5 C 8506 2.51 5 N 2801 2.21 5 O 3421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15047 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 802 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'MLY:plan-1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 717 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 802 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'MLY:plan-1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 652 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2974 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3012 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3103 Classifications: {'peptide': 451} Incomplete info: {'backbone_only': 116} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 499 Unresolved non-hydrogen angles: 725 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 157 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 9, 'ARG:plan': 9, 'ASP:plan': 7, 'GLU:plan': 6, 'HIS:plan': 2, 'TYR:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 230 Time building chain proxies: 3.32, per 1000 atoms: 0.22 Number of scatterers: 15047 At special positions: 0 Unit cell: (102.82, 137.8, 115.54, 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 27 16.00 P 292 15.00 O 3421 8.00 N 2801 7.00 C 8506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 505.4 milliseconds 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2032 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 12 sheets defined 69.6% alpha, 2.8% beta 137 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.516A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.686A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.508A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 Processing helix chain 'E' and resid 42 through 57 removed outlier: 3.964A pdb=" N VAL E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.742A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.954A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.455A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.720A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 10 Processing helix chain 'K' and resid 15 through 27 Processing helix chain 'K' and resid 33 through 49 Processing helix chain 'K' and resid 82 through 101 Processing helix chain 'K' and resid 102 through 106 Processing helix chain 'K' and resid 114 through 128 removed outlier: 3.535A pdb=" N VAL K 118 " --> pdb=" O SER K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 149 removed outlier: 3.566A pdb=" N PHE K 146 " --> pdb=" O SER K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 168 Processing helix chain 'K' and resid 211 through 217 Processing helix chain 'K' and resid 222 through 226 Processing helix chain 'K' and resid 231 through 242 Processing helix chain 'K' and resid 253 through 270 Processing helix chain 'K' and resid 271 through 275 removed outlier: 3.694A pdb=" N ARG K 275 " --> pdb=" O HIS K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 276 through 290 Processing helix chain 'K' and resid 297 through 313 removed outlier: 3.640A pdb=" N TYR K 313 " --> pdb=" O ALA K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 318 through 331 removed outlier: 3.709A pdb=" N ASN K 331 " --> pdb=" O TYR K 327 " (cutoff:3.500A) Processing helix chain 'K' and resid 333 through 349 removed outlier: 3.678A pdb=" N ALA K 337 " --> pdb=" O ASN K 333 " (cutoff:3.500A) Processing helix chain 'K' and resid 357 through 370 removed outlier: 3.875A pdb=" N TYR K 361 " --> pdb=" O ASP K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 384 removed outlier: 3.736A pdb=" N ASN K 374 " --> pdb=" O ASP K 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 406 through 425 Processing helix chain 'K' and resid 433 through 447 removed outlier: 3.954A pdb=" N PHE K 439 " --> pdb=" O GLY K 435 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE K 447 " --> pdb=" O SER K 443 " (cutoff:3.500A) Processing helix chain 'K' and resid 448 through 454 removed outlier: 3.738A pdb=" N LYS K 454 " --> pdb=" O GLN K 450 " (cutoff:3.500A) Processing helix chain 'K' and resid 557 through 565 removed outlier: 3.987A pdb=" N MET K 561 " --> pdb=" O LYS K 557 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU K 563 " --> pdb=" O LYS K 559 " (cutoff:3.500A) Processing helix chain 'K' and resid 571 through 581 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.030A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.831A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.760A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.231A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.314A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 192 through 194 removed outlier: 3.567A pdb=" N GLN K 192 " --> pdb=" O PHE K 186 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA K 194 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL K 184 " --> pdb=" O ALA K 194 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 456 through 458 removed outlier: 5.685A pdb=" N ARG K 456 " --> pdb=" O LEU K 551 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 607 hydrogen bonds defined for protein. 1794 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 352 hydrogen bonds 704 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 3.58 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2751 1.33 - 1.45: 5070 1.45 - 1.57: 7464 1.57 - 1.69: 582 1.69 - 1.81: 45 Bond restraints: 15912 Sorted by residual: bond pdb=" C3' DG I 101 " pdb=" O3' DG I 101 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.33e+01 bond pdb=" C3' DC I 17 " pdb=" C2' DC I 17 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DA J 40 " pdb=" O3' DA J 40 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.13e+01 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.435 1.478 -0.043 1.30e-02 5.92e+03 1.11e+01 bond pdb=" C3' DT I 9 " pdb=" C2' DT I 9 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 ... (remaining 15907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 20523 1.24 - 2.48: 1906 2.48 - 3.73: 256 3.73 - 4.97: 26 4.97 - 6.21: 11 Bond angle restraints: 22722 Sorted by residual: angle pdb=" N3 DT J 15 " pdb=" C4 DT J 15 " pdb=" O4 DT J 15 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.12e+01 angle pdb=" N3 DT I 75 " pdb=" C4 DT I 75 " pdb=" O4 DT I 75 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" O4' DC J 46 " pdb=" C4' DC J 46 " pdb=" C3' DC J 46 " ideal model delta sigma weight residual 106.00 103.35 2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I 115 " pdb=" C4 DT I 115 " pdb=" O4 DT I 115 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 ... (remaining 22717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.14: 7129 34.14 - 68.29: 1442 68.29 - 102.43: 31 102.43 - 136.58: 0 136.58 - 170.72: 3 Dihedral angle restraints: 8605 sinusoidal: 5330 harmonic: 3275 Sorted by residual: dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DG J 16 " ideal model delta sinusoidal sigma weight residual 220.00 49.28 170.72 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA LEU K 177 " pdb=" C LEU K 177 " pdb=" N SER K 178 " pdb=" CA SER K 178 " ideal model delta harmonic sigma weight residual 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 81.15 138.85 1 3.50e+01 8.16e-04 1.37e+01 ... (remaining 8602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1586 0.040 - 0.081: 670 0.081 - 0.121: 215 0.121 - 0.161: 37 0.161 - 0.201: 2 Chirality restraints: 2510 Sorted by residual: chirality pdb=" C3' DT J 15 " pdb=" C4' DT J 15 " pdb=" O3' DT J 15 " pdb=" C2' DT J 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" C3' DC I 82 " pdb=" C4' DC I 82 " pdb=" O3' DC I 82 " pdb=" C2' DC I 82 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" C3' DT J 50 " pdb=" C4' DT J 50 " pdb=" O3' DT J 50 " pdb=" C2' DT J 50 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.22e-01 ... (remaining 2507 not shown) Planarity restraints: 1918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO C 80 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 87 " -0.025 2.00e-02 2.50e+03 1.21e-02 3.64e+00 pdb=" N1 DT I 87 " 0.025 2.00e-02 2.50e+03 pdb=" C2 DT I 87 " 0.005 2.00e-02 2.50e+03 pdb=" O2 DT I 87 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DT I 87 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT I 87 " -0.006 2.00e-02 2.50e+03 pdb=" O4 DT I 87 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DT I 87 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 87 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DT I 87 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 102 " -0.024 2.00e-02 2.50e+03 1.04e-02 3.27e+00 pdb=" N9 DG I 102 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DG I 102 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 102 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 102 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 102 " -0.002 2.00e-02 2.50e+03 pdb=" O6 DG I 102 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 102 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 102 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 102 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 102 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 102 " 0.003 2.00e-02 2.50e+03 ... (remaining 1915 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1415 2.73 - 3.28: 13870 3.28 - 3.82: 28267 3.82 - 4.36: 34444 4.36 - 4.90: 50530 Nonbonded interactions: 128526 Sorted by model distance: nonbonded pdb=" O ASP K 172 " pdb=" OD1 ASP K 172 " model vdw 2.193 3.040 nonbonded pdb=" NH2 ARG B 78 " pdb=" OD2 ASP B 85 " model vdw 2.220 3.120 nonbonded pdb=" NH2 ARG A 40 " pdb=" O2 DT J 83 " model vdw 2.223 3.120 nonbonded pdb=" OG SER H 56 " pdb=" OP2 DC J 20 " model vdw 2.229 3.040 nonbonded pdb=" O ASP K 370 " pdb=" ND2 ASN K 374 " model vdw 2.230 3.120 ... (remaining 128521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 21 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 32 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 59 through 124)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.260 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 0.049 15912 Z= 0.565 Angle : 0.751 6.209 22722 Z= 0.623 Chirality : 0.048 0.201 2510 Planarity : 0.005 0.054 1918 Dihedral : 26.207 170.722 6573 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.11 % Allowed : 6.38 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.24), residues: 1179 helix: 1.61 (0.18), residues: 811 sheet: -1.39 (1.86), residues: 10 loop : -0.78 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 72 TYR 0.013 0.002 TYR G 57 PHE 0.012 0.002 PHE C 25 TRP 0.007 0.001 TRP K 341 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00757 / 0.57 (15912) covalent geometry : angle 0.75078 / 0.62 (22722) hydrogen bonds : bond 0.11521 / 7.63 ( 959) hydrogen bonds : angle 4.28322 / 3.01 ( 2498) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.456 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 200 average time/residue: 0.1530 time to fit residues: 43.8499 Evaluate side-chains 159 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.097838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.062979 restraints weight = 45153.306| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.46 r_work: 0.2827 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15912 Z= 0.198 Angle : 0.674 6.872 22722 Z= 0.379 Chirality : 0.046 0.372 2510 Planarity : 0.005 0.053 1918 Dihedral : 29.748 171.850 4521 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.13 % Allowed : 11.42 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.24), residues: 1179 helix: 1.95 (0.18), residues: 824 sheet: -2.53 (1.27), residues: 16 loop : -0.88 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.023 0.002 TYR D 42 PHE 0.020 0.002 PHE K 186 TRP 0.008 0.001 TRP K 183 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.20 (15912) covalent geometry : angle 0.67361 / 0.38 (22722) hydrogen bonds : bond 0.05075 / 3.46 ( 959) hydrogen bonds : angle 3.57094 / 2.53 ( 2498) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8713 (mt-10) REVERT: B 80 THR cc_start: 0.9601 (OUTLIER) cc_final: 0.9303 (p) REVERT: B 88 TYR cc_start: 0.9273 (m-10) cc_final: 0.8993 (m-80) REVERT: C 91 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7654 (tm-30) REVERT: C 92 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8816 (mm-30) REVERT: D 42 TYR cc_start: 0.8367 (t80) cc_final: 0.8092 (t80) REVERT: D 68 ASP cc_start: 0.9242 (t0) cc_final: 0.8928 (t0) REVERT: E 90 MET cc_start: 0.8857 (mmp) cc_final: 0.8657 (mmt) REVERT: G 16 THR cc_start: 0.9402 (OUTLIER) cc_final: 0.9132 (p) REVERT: G 90 ASP cc_start: 0.8399 (t0) cc_final: 0.8168 (t0) REVERT: H 86 ARG cc_start: 0.8900 (mmt-90) cc_final: 0.8504 (mmt90) REVERT: H 93 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8308 (mp0) REVERT: H 105 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8689 (mm-30) REVERT: K 234 MET cc_start: 0.9251 (mmm) cc_final: 0.8944 (mpp) REVERT: K 283 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9396 (tp) REVERT: K 366 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8420 (tp30) REVERT: K 370 ASP cc_start: 0.8602 (m-30) cc_final: 0.7984 (m-30) REVERT: K 561 MET cc_start: 0.8954 (mpp) cc_final: 0.8606 (mpp) outliers start: 19 outliers final: 8 residues processed: 184 average time/residue: 0.1118 time to fit residues: 30.7562 Evaluate side-chains 171 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain K residue 283 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 372 ILE Chi-restraints excluded: chain K residue 375 LEU Chi-restraints excluded: chain K residue 579 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.097164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.062062 restraints weight = 45271.123| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.55 r_work: 0.2812 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15912 Z= 0.202 Angle : 0.622 6.632 22722 Z= 0.356 Chirality : 0.044 0.364 2510 Planarity : 0.004 0.055 1918 Dihedral : 29.686 171.952 4521 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.24 % Allowed : 12.43 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.25), residues: 1179 helix: 2.25 (0.18), residues: 824 sheet: -2.32 (1.33), residues: 16 loop : -0.85 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.012 0.001 TYR G 57 PHE 0.010 0.001 PHE K 159 TRP 0.006 0.001 TRP K 265 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.20 (15912) covalent geometry : angle 0.62181 / 0.36 (22722) hydrogen bonds : bond 0.04714 / 3.22 ( 959) hydrogen bonds : angle 3.37805 / 2.41 ( 2498) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8740 (mt-10) REVERT: B 80 THR cc_start: 0.9565 (OUTLIER) cc_final: 0.9327 (p) REVERT: B 88 TYR cc_start: 0.9326 (m-10) cc_final: 0.9042 (m-80) REVERT: C 90 ASP cc_start: 0.8547 (t0) cc_final: 0.8274 (t0) REVERT: C 91 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7710 (tm-30) REVERT: D 42 TYR cc_start: 0.8381 (t80) cc_final: 0.8068 (t80) REVERT: D 68 ASP cc_start: 0.9315 (t0) cc_final: 0.8929 (t0) REVERT: D 106 LEU cc_start: 0.9312 (mt) cc_final: 0.9097 (mt) REVERT: E 90 MET cc_start: 0.8858 (mmp) cc_final: 0.8654 (mmt) REVERT: F 88 TYR cc_start: 0.8874 (m-10) cc_final: 0.8652 (m-80) REVERT: G 16 THR cc_start: 0.9420 (OUTLIER) cc_final: 0.9132 (p) REVERT: G 90 ASP cc_start: 0.8448 (t0) cc_final: 0.8091 (t0) REVERT: H 68 ASP cc_start: 0.9166 (t0) cc_final: 0.8783 (t0) REVERT: H 79 ARG cc_start: 0.8773 (ttm110) cc_final: 0.8549 (mtp-110) REVERT: H 86 ARG cc_start: 0.8940 (mmt-90) cc_final: 0.8574 (mmt90) REVERT: H 93 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8267 (mp0) REVERT: H 105 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8708 (mm-30) REVERT: K 366 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8392 (tp30) REVERT: K 370 ASP cc_start: 0.8613 (m-30) cc_final: 0.7996 (m-30) REVERT: K 424 GLU cc_start: 0.9110 (tt0) cc_final: 0.8907 (tt0) REVERT: K 561 MET cc_start: 0.8975 (mpp) cc_final: 0.8674 (mpp) outliers start: 20 outliers final: 8 residues processed: 178 average time/residue: 0.1231 time to fit residues: 32.6938 Evaluate side-chains 170 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 372 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 61 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 74 optimal weight: 40.0000 chunk 103 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 84 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.097290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.062073 restraints weight = 44988.270| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.50 r_work: 0.2819 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15912 Z= 0.176 Angle : 0.604 6.408 22722 Z= 0.347 Chirality : 0.043 0.366 2510 Planarity : 0.004 0.056 1918 Dihedral : 29.656 171.822 4521 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.90 % Allowed : 13.66 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.25), residues: 1179 helix: 2.37 (0.18), residues: 824 sheet: -2.12 (1.38), residues: 16 loop : -0.80 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.012 0.001 TYR D 40 PHE 0.018 0.001 PHE K 186 TRP 0.006 0.001 TRP K 265 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.18 (15912) covalent geometry : angle 0.60415 / 0.35 (22722) hydrogen bonds : bond 0.04339 / 2.97 ( 959) hydrogen bonds : angle 3.25858 / 2.33 ( 2498) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8745 (mt-10) REVERT: B 80 THR cc_start: 0.9518 (OUTLIER) cc_final: 0.9316 (p) REVERT: B 88 TYR cc_start: 0.9333 (m-10) cc_final: 0.9032 (m-80) REVERT: C 73 ASN cc_start: 0.9094 (t0) cc_final: 0.8623 (t0) REVERT: C 90 ASP cc_start: 0.8523 (t0) cc_final: 0.8215 (t0) REVERT: D 42 TYR cc_start: 0.8452 (t80) cc_final: 0.8083 (t80) REVERT: D 62 MET cc_start: 0.9268 (mmt) cc_final: 0.9014 (mmt) REVERT: D 93 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8520 (mt-10) REVERT: D 106 LEU cc_start: 0.9302 (mt) cc_final: 0.9100 (mt) REVERT: F 93 GLN cc_start: 0.9257 (mm-40) cc_final: 0.9024 (mm-40) REVERT: G 90 ASP cc_start: 0.8413 (t0) cc_final: 0.7819 (t70) REVERT: H 68 ASP cc_start: 0.9146 (t0) cc_final: 0.8943 (t0) REVERT: H 83 TYR cc_start: 0.8395 (m-10) cc_final: 0.8191 (m-10) REVERT: H 86 ARG cc_start: 0.8929 (mmt-90) cc_final: 0.8587 (mmt90) REVERT: H 93 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: H 105 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8658 (mm-30) REVERT: K 239 MET cc_start: 0.9201 (ttt) cc_final: 0.8995 (ttt) REVERT: K 366 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8392 (tp30) REVERT: K 370 ASP cc_start: 0.8575 (m-30) cc_final: 0.7964 (m-30) REVERT: K 424 GLU cc_start: 0.9050 (tt0) cc_final: 0.8849 (tt0) REVERT: K 561 MET cc_start: 0.8936 (mpp) cc_final: 0.8643 (mpp) outliers start: 17 outliers final: 9 residues processed: 179 average time/residue: 0.1215 time to fit residues: 32.3990 Evaluate side-chains 174 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 372 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 75 optimal weight: 20.0000 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 0.0670 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 98 optimal weight: 40.0000 chunk 85 optimal weight: 50.0000 chunk 139 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 overall best weight: 1.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.097780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.062525 restraints weight = 44925.639| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.56 r_work: 0.2826 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15912 Z= 0.141 Angle : 0.580 10.638 22722 Z= 0.335 Chirality : 0.041 0.364 2510 Planarity : 0.004 0.055 1918 Dihedral : 29.573 171.354 4521 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.13 % Allowed : 14.89 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.25), residues: 1179 helix: 2.50 (0.18), residues: 825 sheet: -1.97 (1.41), residues: 16 loop : -0.71 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.012 0.001 TYR D 40 PHE 0.009 0.001 PHE E 67 TRP 0.008 0.001 TRP K 265 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (15912) covalent geometry : angle 0.58036 / 0.34 (22722) hydrogen bonds : bond 0.04022 / 2.77 ( 959) hydrogen bonds : angle 3.09971 / 2.22 ( 2498) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9333 (m-10) cc_final: 0.9044 (m-80) REVERT: C 73 ASN cc_start: 0.9096 (t0) cc_final: 0.8601 (t0) REVERT: C 90 ASP cc_start: 0.8460 (t0) cc_final: 0.8088 (t0) REVERT: C 101 THR cc_start: 0.9634 (OUTLIER) cc_final: 0.9416 (p) REVERT: D 42 TYR cc_start: 0.8479 (t80) cc_final: 0.8108 (t80) REVERT: D 62 MET cc_start: 0.9302 (mmt) cc_final: 0.8998 (mmt) REVERT: D 93 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8594 (mt-10) REVERT: F 93 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8952 (mm-40) REVERT: G 90 ASP cc_start: 0.8357 (t0) cc_final: 0.7705 (t70) REVERT: H 68 ASP cc_start: 0.9265 (t0) cc_final: 0.9013 (t0) REVERT: H 83 TYR cc_start: 0.8052 (m-10) cc_final: 0.7825 (m-10) REVERT: H 86 ARG cc_start: 0.8956 (mmt-90) cc_final: 0.8595 (mmt90) REVERT: H 93 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: H 105 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8673 (mm-30) REVERT: K 239 MET cc_start: 0.9313 (ttt) cc_final: 0.9101 (ttt) REVERT: K 278 MET cc_start: 0.7972 (ttt) cc_final: 0.7531 (tmm) REVERT: K 280 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9190 (mp) REVERT: K 366 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8367 (tp30) REVERT: K 370 ASP cc_start: 0.8663 (m-30) cc_final: 0.8003 (m-30) REVERT: K 424 GLU cc_start: 0.9101 (tt0) cc_final: 0.8830 (tt0) REVERT: K 561 MET cc_start: 0.8934 (mpp) cc_final: 0.8600 (mpp) outliers start: 19 outliers final: 8 residues processed: 187 average time/residue: 0.1272 time to fit residues: 35.2789 Evaluate side-chains 176 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 280 LEU Chi-restraints excluded: chain K residue 366 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 88 optimal weight: 30.0000 chunk 22 optimal weight: 1.9990 chunk 111 optimal weight: 50.0000 chunk 83 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 84 ASN E 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.097782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.063666 restraints weight = 44264.410| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.49 r_work: 0.2851 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15912 Z= 0.136 Angle : 0.581 12.111 22722 Z= 0.334 Chirality : 0.041 0.364 2510 Planarity : 0.004 0.057 1918 Dihedral : 29.536 170.923 4521 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.58 % Allowed : 16.24 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.25), residues: 1179 helix: 2.57 (0.18), residues: 825 sheet: -2.05 (1.41), residues: 16 loop : -0.66 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.010 0.001 TYR G 57 PHE 0.022 0.001 PHE K 186 TRP 0.007 0.001 TRP K 265 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (15912) covalent geometry : angle 0.58054 / 0.33 (22722) hydrogen bonds : bond 0.03919 / 2.71 ( 959) hydrogen bonds : angle 3.02771 / 2.18 ( 2498) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9321 (m-10) cc_final: 0.9006 (m-80) REVERT: C 35 ARG cc_start: 0.9271 (tpp80) cc_final: 0.8831 (tpp80) REVERT: C 73 ASN cc_start: 0.9080 (t0) cc_final: 0.8590 (t0) REVERT: C 90 ASP cc_start: 0.8459 (t0) cc_final: 0.8051 (t0) REVERT: C 101 THR cc_start: 0.9622 (OUTLIER) cc_final: 0.9402 (p) REVERT: D 42 TYR cc_start: 0.8443 (t80) cc_final: 0.8111 (t80) REVERT: D 62 MET cc_start: 0.9319 (mmt) cc_final: 0.9014 (mmt) REVERT: D 93 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8586 (mt-10) REVERT: E 50 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8397 (mt-10) REVERT: G 90 ASP cc_start: 0.8384 (t0) cc_final: 0.7731 (t70) REVERT: H 68 ASP cc_start: 0.9277 (t0) cc_final: 0.9035 (t0) REVERT: H 86 ARG cc_start: 0.8932 (mmt-90) cc_final: 0.8542 (mmt90) REVERT: H 93 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: K 239 MET cc_start: 0.9310 (ttt) cc_final: 0.9098 (ttt) REVERT: K 278 MET cc_start: 0.8006 (ttt) cc_final: 0.7551 (tmm) REVERT: K 280 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9190 (mp) REVERT: K 366 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8447 (tp30) REVERT: K 370 ASP cc_start: 0.8658 (m-30) cc_final: 0.7991 (m-30) REVERT: K 424 GLU cc_start: 0.9098 (tt0) cc_final: 0.8817 (tt0) REVERT: K 561 MET cc_start: 0.8923 (mpp) cc_final: 0.8594 (mpp) outliers start: 23 outliers final: 11 residues processed: 189 average time/residue: 0.1104 time to fit residues: 31.4478 Evaluate side-chains 177 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 280 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 372 ILE Chi-restraints excluded: chain K residue 579 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 72 optimal weight: 50.0000 chunk 55 optimal weight: 0.1980 chunk 25 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.097001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.062983 restraints weight = 44762.263| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.48 r_work: 0.2825 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15912 Z= 0.192 Angle : 0.616 9.882 22722 Z= 0.347 Chirality : 0.042 0.368 2510 Planarity : 0.004 0.055 1918 Dihedral : 29.635 170.740 4518 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.46 % Allowed : 16.91 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.25), residues: 1179 helix: 2.58 (0.18), residues: 825 sheet: -2.01 (1.42), residues: 16 loop : -0.60 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.022 0.001 TYR H 83 PHE 0.009 0.001 PHE K 238 TRP 0.007 0.001 TRP K 220 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (15912) covalent geometry : angle 0.61639 / 0.35 (22722) hydrogen bonds : bond 0.04254 / 2.91 ( 959) hydrogen bonds : angle 3.12474 / 2.24 ( 2498) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9349 (m-10) cc_final: 0.9026 (m-80) REVERT: C 35 ARG cc_start: 0.9292 (tpp80) cc_final: 0.8856 (tpp80) REVERT: C 73 ASN cc_start: 0.9069 (t0) cc_final: 0.8575 (t0) REVERT: C 90 ASP cc_start: 0.8482 (t0) cc_final: 0.8094 (t0) REVERT: C 101 THR cc_start: 0.9601 (OUTLIER) cc_final: 0.9368 (p) REVERT: C 110 ASN cc_start: 0.8366 (t0) cc_final: 0.7409 (p0) REVERT: D 42 TYR cc_start: 0.8557 (t80) cc_final: 0.8177 (t80) REVERT: D 62 MET cc_start: 0.9310 (mmt) cc_final: 0.9000 (mmt) REVERT: D 93 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8562 (mt-10) REVERT: G 90 ASP cc_start: 0.8479 (t0) cc_final: 0.7784 (t70) REVERT: H 68 ASP cc_start: 0.9271 (t0) cc_final: 0.9009 (t0) REVERT: H 86 ARG cc_start: 0.8920 (mmt-90) cc_final: 0.8590 (mmt90) REVERT: H 93 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: K 278 MET cc_start: 0.7964 (ttt) cc_final: 0.7579 (tmm) REVERT: K 280 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9246 (mp) REVERT: K 366 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8486 (tp30) REVERT: K 370 ASP cc_start: 0.8639 (m-30) cc_final: 0.8011 (m-30) REVERT: K 424 GLU cc_start: 0.9101 (tt0) cc_final: 0.8831 (tt0) REVERT: K 561 MET cc_start: 0.8966 (mpp) cc_final: 0.8658 (mpp) outliers start: 22 outliers final: 10 residues processed: 179 average time/residue: 0.1187 time to fit residues: 31.6732 Evaluate side-chains 171 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 280 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 372 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 77 optimal weight: 20.0000 chunk 72 optimal weight: 50.0000 chunk 129 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 75 optimal weight: 20.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.097494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.063388 restraints weight = 44985.572| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.43 r_work: 0.2845 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15912 Z= 0.151 Angle : 0.594 9.931 22722 Z= 0.339 Chirality : 0.041 0.365 2510 Planarity : 0.004 0.055 1918 Dihedral : 29.587 170.570 4518 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.63 % Rotamer: Outliers : 2.02 % Allowed : 17.92 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.25), residues: 1179 helix: 2.59 (0.18), residues: 826 sheet: -1.99 (1.43), residues: 16 loop : -0.49 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 86 TYR 0.011 0.001 TYR G 57 PHE 0.023 0.001 PHE K 186 TRP 0.007 0.001 TRP K 220 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (15912) covalent geometry : angle 0.59442 / 0.34 (22722) hydrogen bonds : bond 0.03924 / 2.70 ( 959) hydrogen bonds : angle 3.03387 / 2.18 ( 2498) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9314 (m-10) cc_final: 0.8981 (m-80) REVERT: C 35 ARG cc_start: 0.9288 (tpp80) cc_final: 0.8846 (tpp80) REVERT: C 73 ASN cc_start: 0.9088 (t0) cc_final: 0.8600 (t0) REVERT: C 90 ASP cc_start: 0.8474 (t0) cc_final: 0.8121 (t0) REVERT: C 101 THR cc_start: 0.9600 (OUTLIER) cc_final: 0.9361 (p) REVERT: C 110 ASN cc_start: 0.8387 (t0) cc_final: 0.7527 (p0) REVERT: D 42 TYR cc_start: 0.8495 (t80) cc_final: 0.8130 (t80) REVERT: D 62 MET cc_start: 0.9284 (mmt) cc_final: 0.8989 (mmt) REVERT: D 93 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8565 (mt-10) REVERT: E 76 GLN cc_start: 0.9020 (tp40) cc_final: 0.8802 (tm-30) REVERT: F 88 TYR cc_start: 0.8857 (m-10) cc_final: 0.8282 (m-10) REVERT: G 90 ASP cc_start: 0.8395 (t0) cc_final: 0.7723 (t70) REVERT: H 68 ASP cc_start: 0.9261 (t0) cc_final: 0.9013 (t0) REVERT: H 83 TYR cc_start: 0.8097 (m-10) cc_final: 0.6778 (m-80) REVERT: H 86 ARG cc_start: 0.8913 (mmt-90) cc_final: 0.8594 (mmt90) REVERT: H 93 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: K 280 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9209 (mp) REVERT: K 366 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8527 (tp30) REVERT: K 370 ASP cc_start: 0.8590 (m-30) cc_final: 0.7981 (m-30) REVERT: K 424 GLU cc_start: 0.9067 (tt0) cc_final: 0.8795 (tt0) REVERT: K 561 MET cc_start: 0.8946 (mpp) cc_final: 0.8632 (mpp) REVERT: K 571 ASN cc_start: 0.8883 (t0) cc_final: 0.8615 (t0) outliers start: 18 outliers final: 11 residues processed: 176 average time/residue: 0.1153 time to fit residues: 30.2893 Evaluate side-chains 176 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 280 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 372 ILE Chi-restraints excluded: chain K residue 579 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 17 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 128 optimal weight: 0.3980 chunk 95 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 79 optimal weight: 20.0000 chunk 57 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 109 optimal weight: 8.9990 chunk 94 optimal weight: 11.9990 overall best weight: 4.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.095661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.061426 restraints weight = 45310.257| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.48 r_work: 0.2788 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 15912 Z= 0.306 Angle : 0.697 9.727 22722 Z= 0.381 Chirality : 0.045 0.374 2510 Planarity : 0.004 0.058 1918 Dihedral : 29.796 170.630 4518 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.80 % Favored : 97.12 % Rotamer: Outliers : 1.79 % Allowed : 17.81 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.25), residues: 1179 helix: 2.38 (0.18), residues: 826 sheet: -1.85 (1.43), residues: 16 loop : -0.61 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 86 TYR 0.021 0.002 TYR H 83 PHE 0.014 0.002 PHE C 25 TRP 0.009 0.002 TRP K 220 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.31 (15912) covalent geometry : angle 0.69743 / 0.38 (22722) hydrogen bonds : bond 0.04997 / 3.40 ( 959) hydrogen bonds : angle 3.34077 / 2.39 ( 2498) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: C 35 ARG cc_start: 0.9305 (tpp80) cc_final: 0.8875 (tpp80) REVERT: C 73 ASN cc_start: 0.9026 (t0) cc_final: 0.8527 (t0) REVERT: C 90 ASP cc_start: 0.8613 (t0) cc_final: 0.8200 (t0) REVERT: C 101 THR cc_start: 0.9602 (OUTLIER) cc_final: 0.9330 (p) REVERT: C 110 ASN cc_start: 0.8424 (t0) cc_final: 0.7534 (p0) REVERT: D 33 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.7292 (ttm-80) REVERT: D 42 TYR cc_start: 0.8624 (t80) cc_final: 0.8287 (t80) REVERT: D 93 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8584 (mt-10) REVERT: E 50 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8391 (mt-10) REVERT: E 76 GLN cc_start: 0.9104 (tp40) cc_final: 0.8843 (tm-30) REVERT: G 90 ASP cc_start: 0.8609 (t0) cc_final: 0.7786 (t0) REVERT: H 68 ASP cc_start: 0.9287 (t0) cc_final: 0.9023 (t0) REVERT: H 86 ARG cc_start: 0.8943 (mmt-90) cc_final: 0.8604 (mmt90) REVERT: H 93 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: K 366 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8435 (tp30) REVERT: K 370 ASP cc_start: 0.8624 (m-30) cc_final: 0.7974 (m-30) REVERT: K 424 GLU cc_start: 0.9106 (tt0) cc_final: 0.8862 (tt0) REVERT: K 561 MET cc_start: 0.8980 (mpp) cc_final: 0.8681 (mpp) REVERT: K 571 ASN cc_start: 0.8871 (t0) cc_final: 0.8574 (t0) outliers start: 16 outliers final: 12 residues processed: 167 average time/residue: 0.1075 time to fit residues: 26.6952 Evaluate side-chains 169 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 372 ILE Chi-restraints excluded: chain K residue 579 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 139 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 124 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.097415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.063007 restraints weight = 45078.837| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.54 r_work: 0.2836 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15912 Z= 0.130 Angle : 0.605 11.127 22722 Z= 0.344 Chirality : 0.041 0.363 2510 Planarity : 0.004 0.054 1918 Dihedral : 29.635 170.467 4518 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.12 % Favored : 97.79 % Rotamer: Outliers : 1.46 % Allowed : 18.03 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.25), residues: 1179 helix: 2.55 (0.18), residues: 826 sheet: -1.76 (1.46), residues: 16 loop : -0.46 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.027 0.001 TYR H 83 PHE 0.023 0.001 PHE K 186 TRP 0.007 0.001 TRP K 265 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.13 (15912) covalent geometry : angle 0.60540 / 0.34 (22722) hydrogen bonds : bond 0.03886 / 2.67 ( 959) hydrogen bonds : angle 3.04392 / 2.19 ( 2498) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.8841 (mmm) cc_final: 0.8246 (tmm) REVERT: B 88 TYR cc_start: 0.9333 (m-10) cc_final: 0.8811 (m-80) REVERT: C 35 ARG cc_start: 0.9308 (tpp80) cc_final: 0.8870 (tpp80) REVERT: C 73 ASN cc_start: 0.9066 (t0) cc_final: 0.8585 (t0) REVERT: C 90 ASP cc_start: 0.8496 (t0) cc_final: 0.8142 (t0) REVERT: C 101 THR cc_start: 0.9584 (OUTLIER) cc_final: 0.9340 (p) REVERT: C 110 ASN cc_start: 0.8412 (t0) cc_final: 0.7556 (p0) REVERT: D 33 ARG cc_start: 0.7702 (ttm-80) cc_final: 0.7386 (ttm-80) REVERT: D 42 TYR cc_start: 0.8476 (t80) cc_final: 0.8133 (t80) REVERT: D 62 MET cc_start: 0.9285 (mmt) cc_final: 0.8984 (mmt) REVERT: D 93 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8595 (mt-10) REVERT: E 50 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8239 (mt-10) REVERT: E 76 GLN cc_start: 0.9026 (tp40) cc_final: 0.8722 (tm-30) REVERT: F 44 LYS cc_start: 0.9405 (mttp) cc_final: 0.9111 (mttt) REVERT: F 88 TYR cc_start: 0.8739 (m-10) cc_final: 0.8213 (m-10) REVERT: G 90 ASP cc_start: 0.8166 (t0) cc_final: 0.7666 (t70) REVERT: G 95 LYS cc_start: 0.9585 (ttmt) cc_final: 0.9346 (ttmm) REVERT: H 68 ASP cc_start: 0.9260 (t0) cc_final: 0.8835 (t0) REVERT: H 83 TYR cc_start: 0.7893 (m-10) cc_final: 0.7151 (m-80) REVERT: H 86 ARG cc_start: 0.8919 (mmt-90) cc_final: 0.8586 (mmt90) REVERT: H 93 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8250 (mp0) REVERT: K 366 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8493 (tp30) REVERT: K 370 ASP cc_start: 0.8612 (m-30) cc_final: 0.7999 (m-30) REVERT: K 561 MET cc_start: 0.8914 (mpp) cc_final: 0.8468 (mpp) REVERT: K 571 ASN cc_start: 0.8872 (t0) cc_final: 0.8575 (t0) outliers start: 13 outliers final: 8 residues processed: 184 average time/residue: 0.1039 time to fit residues: 28.4004 Evaluate side-chains 177 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 372 ILE Chi-restraints excluded: chain K residue 579 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 78 optimal weight: 20.0000 chunk 142 optimal weight: 1.9990 chunk 77 optimal weight: 10.9990 chunk 89 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 87 optimal weight: 50.0000 chunk 133 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 110 optimal weight: 40.0000 chunk 128 optimal weight: 0.9980 chunk 92 optimal weight: 20.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.097032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.062012 restraints weight = 45123.600| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.57 r_work: 0.2816 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15912 Z= 0.182 Angle : 0.622 10.545 22722 Z= 0.349 Chirality : 0.042 0.368 2510 Planarity : 0.004 0.066 1918 Dihedral : 29.635 170.154 4518 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.54 % Favored : 97.37 % Rotamer: Outliers : 1.57 % Allowed : 18.03 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.25), residues: 1179 helix: 2.56 (0.18), residues: 826 sheet: -1.75 (1.45), residues: 16 loop : -0.46 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 86 TYR 0.050 0.002 TYR H 83 PHE 0.010 0.001 PHE K 238 TRP 0.008 0.001 TRP K 220 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (15912) covalent geometry : angle 0.62165 / 0.35 (22722) hydrogen bonds : bond 0.04103 / 2.81 ( 959) hydrogen bonds : angle 3.11719 / 2.24 ( 2498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3391.56 seconds wall clock time: 58 minutes 41.13 seconds (3521.13 seconds total)