Starting phenix.real_space_refine on Sat Aug 23 21:04:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gpn_34195/08_2025/8gpn_34195.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gpn_34195/08_2025/8gpn_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gpn_34195/08_2025/8gpn_34195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gpn_34195/08_2025/8gpn_34195.map" model { file = "/net/cci-nas-00/data/ceres_data/8gpn_34195/08_2025/8gpn_34195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gpn_34195/08_2025/8gpn_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-2.0-5787/lib/python3.9/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: 3.74, per 1000 atoms: 0.25 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: 1.40 Conformation dependent library (CDL) restraints added in 535.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.33 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: 3.93 Time building geometry restraints manager: 1.89 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' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.52e+00 bond pdb=" O3' DT I 58 " pdb=" P DA I 59 " ideal model delta sigma weight residual 1.607 1.581 0.026 1.50e-02 4.44e+03 3.09e+00 bond pdb=" C LEU D 101 " pdb=" N LEU D 102 " ideal model delta sigma weight residual 1.329 1.303 0.026 1.60e-02 3.91e+03 2.54e+00 bond pdb=" CB VAL B 87 " pdb=" CG1 VAL B 87 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.18e+00 bond pdb=" CB MLY A 79 " pdb=" CG MLY A 79 " ideal model delta sigma weight residual 1.527 1.498 0.029 2.00e-02 2.50e+03 2.12e+00 ... (remaining 15907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 21484 1.24 - 2.48: 1095 2.48 - 3.73: 112 3.73 - 4.97: 20 4.97 - 6.21: 11 Bond angle restraints: 22722 Sorted by residual: angle pdb=" O3' DC J 108 " pdb=" C3' DC J 108 " pdb=" C2' DC J 108 " ideal model delta sigma weight residual 111.50 106.90 4.60 1.50e+00 4.44e-01 9.41e+00 angle pdb=" C ASP K 370 " pdb=" N VAL K 371 " pdb=" CA VAL K 371 " ideal model delta sigma weight residual 122.35 118.98 3.37 1.18e+00 7.18e-01 8.15e+00 angle pdb=" C4' DT J 109 " pdb=" C3' DT J 109 " pdb=" O3' DT J 109 " ideal model delta sigma weight residual 110.00 105.94 4.06 1.50e+00 4.44e-01 7.33e+00 angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DG J 16 " ideal model delta sigma weight residual 120.20 124.16 -3.96 1.50e+00 4.44e-01 6.98e+00 angle pdb=" N GLN K 405 " pdb=" CA GLN K 405 " pdb=" C GLN K 405 " ideal model delta sigma weight residual 113.56 109.93 3.63 1.39e+00 5.18e-01 6.81e+00 ... (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 - 0.031: 1518 0.031 - 0.062: 696 0.062 - 0.092: 230 0.092 - 0.123: 52 0.123 - 0.154: 14 Chirality restraints: 2510 Sorted by residual: chirality pdb=" C3' DT J 109 " pdb=" C4' DT J 109 " pdb=" O3' DT J 109 " pdb=" C2' DT J 109 " both_signs ideal model delta sigma weight residual False -2.66 -2.81 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA ILE G 102 " pdb=" N ILE G 102 " pdb=" C ILE G 102 " pdb=" CB ILE G 102 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-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: 1.110 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.320 Find NCS groups from input model: 0.130 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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 : 0.007 0.056 15912 Z= 0.284 Angle : 0.620 6.209 22722 Z= 0.360 Chirality : 0.039 0.154 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 aren 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 covalent geometry : bond 0.00662 (15912) covalent geometry : angle 0.61958 (22722) hydrogen bonds : bond 0.11521 ( 959) hydrogen bonds : angle 4.28322 ( 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 : 0.458 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 200 average time/residue: 0.1572 time to fit residues: 44.0043 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 : 0.450 ------------------------------------------------------------------------------- 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: 10.0000 chunk 107 optimal weight: 50.0000 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3838 r_free = 0.3838 target = 0.097549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.062479 restraints weight = 44785.469| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.58 r_work: 0.2820 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15912 Z= 0.210 Angle : 0.574 6.379 22722 Z= 0.336 Chirality : 0.036 0.147 2510 Planarity : 0.004 0.056 1918 Dihedral : 29.381 172.545 4521 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.02 % Allowed : 11.53 % 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 aren not related in a simple way. whole: 1.94 (0.25), residues: 1179 helix: 2.15 (0.18), residues: 824 sheet: -1.19 (1.95), residues: 10 loop : -0.80 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.016 0.001 TYR B 88 PHE 0.019 0.002 PHE K 186 TRP 0.005 0.001 TRP K 183 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00471 (15912) covalent geometry : angle 0.57434 (22722) hydrogen bonds : bond 0.04287 ( 959) hydrogen bonds : angle 3.34161 ( 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 191 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8717 (mt-10) REVERT: B 80 THR cc_start: 0.9590 (OUTLIER) cc_final: 0.9333 (p) REVERT: B 88 TYR cc_start: 0.9303 (m-80) cc_final: 0.9017 (m-80) REVERT: D 62 MET cc_start: 0.9323 (mmt) cc_final: 0.9100 (mmt) REVERT: D 68 ASP cc_start: 0.9308 (t0) cc_final: 0.9024 (t0) REVERT: D 106 LEU cc_start: 0.9301 (mt) cc_final: 0.9076 (mt) REVERT: D 113 GLU cc_start: 0.9222 (tp30) cc_final: 0.9015 (tp30) REVERT: E 76 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8664 (tm-30) REVERT: E 90 MET cc_start: 0.8875 (mmp) cc_final: 0.8603 (mmt) REVERT: G 16 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.9099 (p) REVERT: G 90 ASP cc_start: 0.8452 (t0) cc_final: 0.8224 (t0) REVERT: H 93 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8296 (mp0) REVERT: H 105 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8734 (mm-30) REVERT: K 366 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8440 (tp30) REVERT: K 370 ASP cc_start: 0.8622 (m-30) cc_final: 0.8032 (m-30) REVERT: K 561 MET cc_start: 0.8962 (mpp) cc_final: 0.8597 (mpp) outliers start: 18 outliers final: 7 residues processed: 184 average time/residue: 0.1295 time to fit residues: 35.1574 Evaluate side-chains 165 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 375 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: 2.9990 chunk 5 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 141 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.097429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.062145 restraints weight = 45517.119| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.57 r_work: 0.2820 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15912 Z= 0.195 Angle : 0.548 6.000 22722 Z= 0.323 Chirality : 0.035 0.143 2510 Planarity : 0.004 0.054 1918 Dihedral : 29.223 171.822 4521 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.68 % Allowed : 12.88 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.25), residues: 1179 helix: 2.39 (0.18), residues: 826 sheet: -2.09 (1.39), residues: 16 loop : -0.77 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.013 0.001 TYR D 40 PHE 0.007 0.001 PHE E 67 TRP 0.007 0.001 TRP K 220 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00436 (15912) covalent geometry : angle 0.54792 (22722) hydrogen bonds : bond 0.03861 ( 959) hydrogen bonds : angle 3.17040 ( 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: 15 poor density : 171 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9327 (m-10) cc_final: 0.9018 (m-80) REVERT: C 35 ARG cc_start: 0.9304 (tpp80) cc_final: 0.8867 (tpp80) REVERT: C 73 ASN cc_start: 0.9098 (t0) cc_final: 0.8628 (t0) REVERT: D 62 MET cc_start: 0.9283 (mmt) cc_final: 0.8990 (mmt) REVERT: D 93 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8548 (mt-10) REVERT: D 106 LEU cc_start: 0.9297 (mt) cc_final: 0.9096 (mt) REVERT: E 76 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8727 (tm-30) REVERT: E 90 MET cc_start: 0.8862 (mmp) cc_final: 0.8612 (mmt) REVERT: E 120 MET cc_start: 0.8581 (mtp) cc_final: 0.8311 (mtt) REVERT: G 90 ASP cc_start: 0.8504 (t0) cc_final: 0.8127 (t0) REVERT: H 83 TYR cc_start: 0.8220 (m-10) cc_final: 0.7864 (m-10) REVERT: H 93 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8254 (mp0) REVERT: K 366 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8459 (tp30) REVERT: K 370 ASP cc_start: 0.8540 (m-30) cc_final: 0.7896 (m-30) REVERT: K 424 GLU cc_start: 0.9064 (tt0) cc_final: 0.8854 (tt0) REVERT: K 561 MET cc_start: 0.8969 (mpp) cc_final: 0.8638 (mpp) outliers start: 15 outliers final: 6 residues processed: 180 average time/residue: 0.1294 time to fit residues: 34.4149 Evaluate side-chains 171 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 93 GLU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 375 LEU 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: 4.9990 chunk 7 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3820 r_free = 0.3820 target = 0.096471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.061861 restraints weight = 45403.477| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.51 r_work: 0.2800 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15912 Z= 0.235 Angle : 0.568 6.976 22722 Z= 0.332 Chirality : 0.036 0.142 2510 Planarity : 0.004 0.054 1918 Dihedral : 29.285 171.736 4521 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.46 % Allowed : 14.33 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.25), residues: 1179 helix: 2.43 (0.18), residues: 826 sheet: -2.07 (1.40), residues: 16 loop : -0.76 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 86 TYR 0.012 0.001 TYR G 57 PHE 0.018 0.002 PHE K 186 TRP 0.005 0.001 TRP K 265 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00527 (15912) covalent geometry : angle 0.56846 (22722) hydrogen bonds : bond 0.04036 ( 959) hydrogen bonds : angle 3.19376 ( 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 181 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9362 (m-10) cc_final: 0.9024 (m-80) REVERT: C 35 ARG cc_start: 0.9328 (tpp80) cc_final: 0.8860 (tpp80) REVERT: C 73 ASN cc_start: 0.9112 (t0) cc_final: 0.8622 (t0) REVERT: C 110 ASN cc_start: 0.8413 (t0) cc_final: 0.7457 (p0) REVERT: D 62 MET cc_start: 0.9306 (mmt) cc_final: 0.8984 (mmt) REVERT: D 106 LEU cc_start: 0.9346 (mt) cc_final: 0.9140 (mt) REVERT: E 76 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8735 (tm-30) REVERT: E 90 MET cc_start: 0.8879 (mmp) cc_final: 0.8629 (mmt) REVERT: G 90 ASP cc_start: 0.8598 (t0) cc_final: 0.8169 (t0) REVERT: H 68 ASP cc_start: 0.9184 (t0) cc_final: 0.8868 (t0) REVERT: H 71 GLU cc_start: 0.8917 (tp30) cc_final: 0.8698 (tm-30) REVERT: H 93 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8243 (mp0) REVERT: K 239 MET cc_start: 0.9277 (ttt) cc_final: 0.9068 (ttt) REVERT: K 366 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8484 (tp30) REVERT: K 370 ASP cc_start: 0.8568 (m-30) cc_final: 0.7916 (m-30) REVERT: K 424 GLU cc_start: 0.9082 (tt0) cc_final: 0.8860 (tt0) REVERT: K 561 MET cc_start: 0.8969 (mpp) cc_final: 0.8669 (mpp) outliers start: 13 outliers final: 8 residues processed: 180 average time/residue: 0.1321 time to fit residues: 34.9488 Evaluate side-chains 170 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR 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 366 GLU Chi-restraints excluded: chain K residue 372 ILE Chi-restraints excluded: chain K residue 375 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 75 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 0.0970 chunk 98 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.098565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.064301 restraints weight = 45191.205| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.51 r_work: 0.2867 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15912 Z= 0.136 Angle : 0.525 7.300 22722 Z= 0.309 Chirality : 0.033 0.142 2510 Planarity : 0.004 0.057 1918 Dihedral : 29.022 170.144 4518 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.68 % Allowed : 15.57 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.25), residues: 1179 helix: 2.64 (0.18), residues: 826 sheet: -2.13 (1.42), residues: 16 loop : -0.57 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 86 TYR 0.012 0.001 TYR D 40 PHE 0.009 0.001 PHE E 67 TRP 0.009 0.001 TRP K 265 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00290 (15912) covalent geometry : angle 0.52503 (22722) hydrogen bonds : bond 0.03318 ( 959) hydrogen bonds : angle 2.87954 ( 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 200 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.423 Fit side-chains REVERT: B 88 TYR cc_start: 0.9298 (m-10) cc_final: 0.8975 (m-80) REVERT: C 35 ARG cc_start: 0.9303 (tpp80) cc_final: 0.8821 (tpp80) REVERT: C 73 ASN cc_start: 0.9148 (t0) cc_final: 0.8679 (t0) REVERT: C 110 ASN cc_start: 0.8444 (t0) cc_final: 0.7603 (p0) REVERT: D 93 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8515 (mt-10) REVERT: E 51 ILE cc_start: 0.8499 (mt) cc_final: 0.8201 (mp) REVERT: E 76 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8687 (tm-30) REVERT: E 90 MET cc_start: 0.8838 (mmp) cc_final: 0.8491 (mmt) REVERT: F 44 LYS cc_start: 0.9364 (mttp) cc_final: 0.9135 (mttt) REVERT: F 96 THR cc_start: 0.9575 (m) cc_final: 0.9347 (p) REVERT: G 90 ASP cc_start: 0.8432 (t0) cc_final: 0.8083 (t70) REVERT: H 68 ASP cc_start: 0.9152 (t0) cc_final: 0.8824 (t0) REVERT: H 71 GLU cc_start: 0.8849 (tp30) cc_final: 0.8623 (tm-30) REVERT: H 83 TYR cc_start: 0.8005 (m-10) cc_final: 0.7714 (m-10) REVERT: H 93 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: K 239 MET cc_start: 0.9310 (ttt) cc_final: 0.9076 (ttt) REVERT: K 366 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8547 (tp30) REVERT: K 370 ASP cc_start: 0.8492 (m-30) cc_final: 0.7867 (m-30) REVERT: K 424 GLU cc_start: 0.8982 (tt0) cc_final: 0.8720 (tt0) REVERT: K 561 MET cc_start: 0.8893 (mpp) cc_final: 0.8563 (mpp) REVERT: K 571 ASN cc_start: 0.8903 (t0) cc_final: 0.8638 (t0) outliers start: 15 outliers final: 5 residues processed: 196 average time/residue: 0.1421 time to fit residues: 40.1622 Evaluate side-chains 173 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 93 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 111 optimal weight: 50.0000 chunk 83 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.098095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.063668 restraints weight = 44895.757| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.45 r_work: 0.2869 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15912 Z= 0.155 Angle : 0.540 12.265 22722 Z= 0.313 Chirality : 0.034 0.142 2510 Planarity : 0.004 0.056 1918 Dihedral : 29.039 170.074 4518 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.90 % Allowed : 16.80 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.25), residues: 1179 helix: 2.66 (0.18), residues: 827 sheet: -2.01 (1.44), residues: 16 loop : -0.42 (0.34), residues: 336 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 0.021 0.001 PHE K 186 TRP 0.007 0.001 TRP K 265 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00340 (15912) covalent geometry : angle 0.53958 (22722) hydrogen bonds : bond 0.03429 ( 959) hydrogen bonds : angle 2.89383 ( 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 190 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.477 Fit side-chains REVERT: B 88 TYR cc_start: 0.9317 (m-10) cc_final: 0.8954 (m-80) REVERT: C 73 ASN cc_start: 0.9133 (t0) cc_final: 0.8673 (t0) REVERT: C 101 THR cc_start: 0.9588 (OUTLIER) cc_final: 0.9363 (p) REVERT: C 110 ASN cc_start: 0.8463 (t0) cc_final: 0.7707 (p0) REVERT: D 62 MET cc_start: 0.9107 (mmt) cc_final: 0.8888 (mmt) REVERT: D 93 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8509 (mt-10) REVERT: E 50 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8021 (tt0) REVERT: E 76 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8684 (tm-30) REVERT: E 90 MET cc_start: 0.8765 (mmp) cc_final: 0.8488 (mmt) REVERT: G 61 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7867 (tm-30) REVERT: G 90 ASP cc_start: 0.8466 (t0) cc_final: 0.7982 (t70) REVERT: H 46 LYS cc_start: 0.9424 (mmmt) cc_final: 0.9103 (mmmm) REVERT: H 68 ASP cc_start: 0.9148 (t0) cc_final: 0.8945 (t0) REVERT: H 71 GLU cc_start: 0.8857 (tp30) cc_final: 0.8626 (tm-30) REVERT: H 93 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: K 234 MET cc_start: 0.9191 (mmm) cc_final: 0.8909 (mpp) REVERT: K 239 MET cc_start: 0.9305 (ttt) cc_final: 0.9043 (ttt) REVERT: K 260 GLN cc_start: 0.9511 (tt0) cc_final: 0.9014 (tp-100) REVERT: K 366 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8526 (tp30) REVERT: K 370 ASP cc_start: 0.8455 (m-30) cc_final: 0.7832 (m-30) REVERT: K 424 GLU cc_start: 0.8965 (tt0) cc_final: 0.8725 (tt0) REVERT: K 561 MET cc_start: 0.8893 (mpp) cc_final: 0.8617 (mpp) REVERT: K 571 ASN cc_start: 0.8911 (t0) cc_final: 0.8680 (t0) outliers start: 17 outliers final: 8 residues processed: 186 average time/residue: 0.1291 time to fit residues: 35.7602 Evaluate side-chains 178 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 59 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 72 optimal weight: 40.0000 chunk 55 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.098137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.063844 restraints weight = 45012.962| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.47 r_work: 0.2868 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15912 Z= 0.154 Angle : 0.544 10.899 22722 Z= 0.314 Chirality : 0.033 0.142 2510 Planarity : 0.004 0.057 1918 Dihedral : 29.009 169.759 4518 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.90 % Allowed : 17.02 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.73 (0.25), residues: 1179 helix: 2.69 (0.18), residues: 827 sheet: -1.80 (1.45), residues: 16 loop : -0.30 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.015 0.001 TYR H 83 PHE 0.006 0.001 PHE E 67 TRP 0.007 0.001 TRP K 220 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00340 (15912) covalent geometry : angle 0.54415 (22722) hydrogen bonds : bond 0.03356 ( 959) hydrogen bonds : angle 2.84555 ( 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 188 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9287 (m-10) cc_final: 0.8896 (m-80) REVERT: C 73 ASN cc_start: 0.9134 (t0) cc_final: 0.8661 (t0) REVERT: C 91 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7655 (tm-30) REVERT: C 101 THR cc_start: 0.9587 (OUTLIER) cc_final: 0.9355 (p) REVERT: C 110 ASN cc_start: 0.8431 (t0) cc_final: 0.7757 (p0) REVERT: D 93 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8540 (mt-10) REVERT: E 50 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8079 (tt0) REVERT: E 51 ILE cc_start: 0.8570 (mt) cc_final: 0.8301 (mp) REVERT: E 76 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8682 (tm-30) REVERT: E 90 MET cc_start: 0.8762 (mmp) cc_final: 0.8534 (mmt) REVERT: G 61 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7710 (tm-30) REVERT: G 90 ASP cc_start: 0.8605 (t0) cc_final: 0.8040 (t0) REVERT: H 46 LYS cc_start: 0.9428 (mmmt) cc_final: 0.9087 (mmmm) REVERT: H 68 ASP cc_start: 0.9181 (t0) cc_final: 0.8969 (t0) REVERT: H 71 GLU cc_start: 0.8904 (tp30) cc_final: 0.8658 (tm-30) REVERT: H 93 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8233 (mp0) REVERT: K 260 GLN cc_start: 0.9539 (tt0) cc_final: 0.9073 (tp-100) REVERT: K 278 MET cc_start: 0.8066 (ttt) cc_final: 0.7607 (tmm) REVERT: K 280 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9349 (mt) REVERT: K 366 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8527 (tp30) REVERT: K 370 ASP cc_start: 0.8463 (m-30) cc_final: 0.7811 (m-30) REVERT: K 424 GLU cc_start: 0.8999 (tt0) cc_final: 0.8736 (tt0) REVERT: K 561 MET cc_start: 0.8880 (mpp) cc_final: 0.8574 (mpp) REVERT: K 571 ASN cc_start: 0.8902 (t0) cc_final: 0.8628 (t0) outliers start: 17 outliers final: 9 residues processed: 184 average time/residue: 0.1250 time to fit residues: 34.3940 Evaluate side-chains 179 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 93 GLU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 11 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 72 optimal weight: 40.0000 chunk 129 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.097408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.062751 restraints weight = 45327.303| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.52 r_work: 0.2837 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15912 Z= 0.196 Angle : 0.570 11.582 22722 Z= 0.327 Chirality : 0.035 0.142 2510 Planarity : 0.004 0.056 1918 Dihedral : 29.106 169.812 4518 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.79 % Allowed : 18.14 % 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 aren not related in a simple way. whole: 2.69 (0.25), residues: 1179 helix: 2.65 (0.18), residues: 826 sheet: -1.70 (1.44), residues: 16 loop : -0.28 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.048 0.002 TYR F 88 PHE 0.021 0.001 PHE K 186 TRP 0.007 0.001 TRP K 220 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00441 (15912) covalent geometry : angle 0.57048 (22722) hydrogen bonds : bond 0.03671 ( 959) hydrogen bonds : angle 2.98431 ( 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 181 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9328 (m-10) cc_final: 0.8940 (m-80) REVERT: C 73 ASN cc_start: 0.9128 (t0) cc_final: 0.8664 (t0) REVERT: C 110 ASN cc_start: 0.8405 (t0) cc_final: 0.7809 (p0) REVERT: D 68 ASP cc_start: 0.9362 (t70) cc_final: 0.8879 (t0) REVERT: D 93 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8534 (mt-10) REVERT: E 50 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8082 (tt0) REVERT: E 76 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8691 (tm-30) REVERT: E 90 MET cc_start: 0.8787 (mmp) cc_final: 0.8573 (mmt) REVERT: F 88 TYR cc_start: 0.8769 (m-80) cc_final: 0.8247 (m-80) REVERT: G 90 ASP cc_start: 0.8611 (t0) cc_final: 0.8376 (t0) REVERT: H 46 LYS cc_start: 0.9429 (mmmt) cc_final: 0.9102 (mmmm) REVERT: H 68 ASP cc_start: 0.9214 (t0) cc_final: 0.8990 (t0) REVERT: H 71 GLU cc_start: 0.8923 (tp30) cc_final: 0.8714 (tm-30) REVERT: H 93 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: K 260 GLN cc_start: 0.9483 (tt0) cc_final: 0.9046 (tp-100) REVERT: K 278 MET cc_start: 0.8101 (ttt) cc_final: 0.7608 (tmm) REVERT: K 280 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9348 (mt) REVERT: K 366 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8548 (tp30) REVERT: K 370 ASP cc_start: 0.8493 (m-30) cc_final: 0.7861 (m-30) REVERT: K 561 MET cc_start: 0.8933 (mpp) cc_final: 0.8643 (mpp) REVERT: K 571 ASN cc_start: 0.8890 (t0) cc_final: 0.8610 (t0) outliers start: 16 outliers final: 10 residues processed: 176 average time/residue: 0.1289 time to fit residues: 33.5307 Evaluate side-chains 177 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 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 93 GLU 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: 0.4980 chunk 135 optimal weight: 10.0000 chunk 128 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.096935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.062277 restraints weight = 45170.015| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.47 r_work: 0.2829 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15912 Z= 0.214 Angle : 0.586 10.226 22722 Z= 0.335 Chirality : 0.035 0.141 2510 Planarity : 0.004 0.056 1918 Dihedral : 29.186 169.627 4518 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.54 % Rotamer: Outliers : 1.79 % Allowed : 18.59 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.25), residues: 1179 helix: 2.60 (0.18), residues: 826 sheet: -1.67 (1.44), residues: 16 loop : -0.26 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 86 TYR 0.048 0.002 TYR F 88 PHE 0.007 0.001 PHE C 25 TRP 0.009 0.001 TRP K 220 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00483 (15912) covalent geometry : angle 0.58552 (22722) hydrogen bonds : bond 0.03786 ( 959) hydrogen bonds : angle 3.05300 ( 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 181 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.471 Fit side-chains REVERT: C 73 ASN cc_start: 0.9095 (t0) cc_final: 0.8621 (t0) REVERT: C 110 ASN cc_start: 0.8422 (t0) cc_final: 0.7838 (p0) REVERT: D 33 ARG cc_start: 0.7644 (ttm-80) cc_final: 0.6938 (ttm-80) REVERT: D 68 ASP cc_start: 0.9362 (t70) cc_final: 0.8879 (t0) REVERT: D 93 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8574 (mt-10) REVERT: E 76 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8895 (tm-30) REVERT: E 90 MET cc_start: 0.8795 (mmp) cc_final: 0.8588 (mmt) REVERT: G 90 ASP cc_start: 0.8601 (t0) cc_final: 0.8329 (t0) REVERT: H 46 LYS cc_start: 0.9423 (mmmt) cc_final: 0.9100 (mmmm) REVERT: H 68 ASP cc_start: 0.9235 (t0) cc_final: 0.9003 (t0) REVERT: H 93 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8217 (mp0) REVERT: K 260 GLN cc_start: 0.9499 (tt0) cc_final: 0.9044 (tp-100) REVERT: K 278 MET cc_start: 0.8111 (ttt) cc_final: 0.7652 (tmm) REVERT: K 280 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9334 (mt) REVERT: K 366 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8528 (tp30) REVERT: K 370 ASP cc_start: 0.8522 (m-30) cc_final: 0.7807 (m-30) REVERT: K 561 MET cc_start: 0.8942 (mpp) cc_final: 0.8648 (mpp) REVERT: K 571 ASN cc_start: 0.8901 (t0) cc_final: 0.8608 (t0) outliers start: 16 outliers final: 12 residues processed: 177 average time/residue: 0.1329 time to fit residues: 34.5132 Evaluate side-chains 178 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 93 GLU 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 375 LEU 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: 0.8980 chunk 30 optimal weight: 0.0770 chunk 25 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.098139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.064244 restraints weight = 44674.970| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.48 r_work: 0.2875 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15912 Z= 0.150 Angle : 0.574 12.798 22722 Z= 0.327 Chirality : 0.034 0.150 2510 Planarity : 0.004 0.057 1918 Dihedral : 29.027 168.587 4518 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.12 % Favored : 97.79 % Rotamer: Outliers : 1.68 % Allowed : 19.60 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.74 (0.25), residues: 1179 helix: 2.66 (0.18), residues: 827 sheet: -1.62 (1.44), residues: 16 loop : -0.18 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.037 0.001 TYR F 88 PHE 0.020 0.001 PHE K 186 TRP 0.007 0.001 TRP K 265 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00331 (15912) covalent geometry : angle 0.57423 (22722) hydrogen bonds : bond 0.03341 ( 959) hydrogen bonds : angle 2.91728 ( 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: 15 poor density : 172 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.8872 (mmm) cc_final: 0.8502 (tmm) REVERT: B 88 TYR cc_start: 0.9233 (m-10) cc_final: 0.8733 (m-80) REVERT: C 35 ARG cc_start: 0.9275 (tpp80) cc_final: 0.8751 (tpp80) REVERT: C 73 ASN cc_start: 0.9147 (t0) cc_final: 0.8726 (t0) REVERT: C 110 ASN cc_start: 0.8428 (t0) cc_final: 0.7886 (p0) REVERT: D 33 ARG cc_start: 0.7633 (ttm-80) cc_final: 0.6979 (ttm-80) REVERT: E 51 ILE cc_start: 0.8475 (mt) cc_final: 0.8226 (mp) REVERT: E 76 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8681 (tm-30) REVERT: F 44 LYS cc_start: 0.9321 (mttp) cc_final: 0.9057 (mttt) REVERT: F 88 TYR cc_start: 0.8520 (m-10) cc_final: 0.8234 (m-80) REVERT: G 61 GLU cc_start: 0.8404 (tp30) cc_final: 0.8186 (tm-30) REVERT: G 90 ASP cc_start: 0.8623 (t0) cc_final: 0.8247 (t0) REVERT: H 46 LYS cc_start: 0.9399 (mmmt) cc_final: 0.9104 (mmmm) REVERT: H 68 ASP cc_start: 0.9244 (t0) cc_final: 0.8890 (t0) REVERT: H 93 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8274 (mp0) REVERT: K 260 GLN cc_start: 0.9485 (tt0) cc_final: 0.9178 (tp-100) REVERT: K 278 MET cc_start: 0.8060 (ttt) cc_final: 0.7595 (tmm) REVERT: K 280 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9287 (mt) REVERT: K 366 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8551 (tp30) REVERT: K 370 ASP cc_start: 0.8531 (m-30) cc_final: 0.7893 (m-30) REVERT: K 571 ASN cc_start: 0.8908 (t0) cc_final: 0.8622 (t0) outliers start: 15 outliers final: 8 residues processed: 182 average time/residue: 0.1304 time to fit residues: 34.8451 Evaluate side-chains 177 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 93 GLU 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 375 LEU 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: 5.9990 chunk 142 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 110 optimal weight: 0.0060 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.097582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.063793 restraints weight = 44837.011| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.49 r_work: 0.2863 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15912 Z= 0.169 Angle : 0.575 11.991 22722 Z= 0.327 Chirality : 0.034 0.141 2510 Planarity : 0.004 0.056 1918 Dihedral : 29.052 168.508 4518 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.12 % Favored : 97.79 % Rotamer: Outliers : 1.34 % Allowed : 19.93 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.77 (0.25), residues: 1179 helix: 2.67 (0.18), residues: 827 sheet: -1.60 (1.43), residues: 16 loop : -0.16 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 86 TYR 0.035 0.001 TYR F 88 PHE 0.009 0.001 PHE K 238 TRP 0.008 0.001 TRP K 265 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00377 (15912) covalent geometry : angle 0.57526 (22722) hydrogen bonds : bond 0.03450 ( 959) hydrogen bonds : angle 2.94867 ( 2498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3957.98 seconds wall clock time: 68 minutes 26.82 seconds (4106.82 seconds total)