Starting phenix.real_space_refine on Fri May 16 17:42:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gpn_34195/05_2025/8gpn_34195.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gpn_34195/05_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_34195/05_2025/8gpn_34195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gpn_34195/05_2025/8gpn_34195.map" model { file = "/net/cci-nas-00/data/ceres_data/8gpn_34195/05_2025/8gpn_34195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gpn_34195/05_2025/8gpn_34195.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 9, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 230 Time building chain proxies: 9.19, per 1000 atoms: 0.61 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: 3.71 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 7.21 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: 7.35 Time building geometry restraints manager: 4.38 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: 0.840 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 42.110 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.810 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (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 TRP 0.007 0.001 TRP K 341 HIS 0.008 0.001 HIS B 75 PHE 0.012 0.002 PHE C 25 TYR 0.013 0.002 TYR G 57 ARG 0.004 0.001 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.11521 ( 959) hydrogen bonds : angle 4.28322 ( 2498) covalent geometry : bond 0.00662 (15912) covalent geometry : angle 0.61958 (22722) *********************** 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 : 1.317 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 200 average time/residue: 0.3149 time to fit residues: 88.0321 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 : 1.231 ------------------------------------------------------------------------------- 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 122 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 131 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.098370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.063595 restraints weight = 44465.456| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.51 r_work: 0.2850 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1357 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= 0.162 Angle : 0.556 6.820 22722 Z= 0.327 Chirality : 0.035 0.148 2510 Planarity : 0.004 0.057 1918 Dihedral : 29.280 172.322 4521 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.34 % Allowed : 12.09 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.25), residues: 1179 helix: 2.22 (0.18), residues: 824 sheet: -1.29 (1.91), residues: 10 loop : -0.78 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 265 HIS 0.006 0.001 HIS B 75 PHE 0.018 0.001 PHE K 186 TYR 0.016 0.001 TYR B 88 ARG 0.007 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 959) hydrogen bonds : angle 3.26069 ( 2498) covalent geometry : bond 0.00354 (15912) covalent geometry : angle 0.55554 (22722) *********************** 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 193 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 THR cc_start: 0.9562 (t) cc_final: 0.9350 (p) REVERT: B 88 TYR cc_start: 0.9255 (m-80) cc_final: 0.8983 (m-10) REVERT: C 35 ARG cc_start: 0.9253 (tpp80) cc_final: 0.8839 (tpp80) REVERT: C 73 ASN cc_start: 0.9098 (t0) cc_final: 0.8658 (t0) REVERT: D 62 MET cc_start: 0.9262 (mmt) cc_final: 0.9010 (mmt) REVERT: D 68 ASP cc_start: 0.9273 (t0) cc_final: 0.8995 (t0) REVERT: D 106 LEU cc_start: 0.9262 (mt) cc_final: 0.9049 (mt) REVERT: E 90 MET cc_start: 0.8845 (mmp) cc_final: 0.8590 (mmt) REVERT: E 123 ASP cc_start: 0.9013 (m-30) cc_final: 0.8813 (m-30) REVERT: F 88 TYR cc_start: 0.8900 (m-10) cc_final: 0.8636 (m-10) REVERT: F 93 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8967 (mm-40) REVERT: G 90 ASP cc_start: 0.8334 (t0) cc_final: 0.8127 (t0) REVERT: H 83 TYR cc_start: 0.8022 (m-10) cc_final: 0.7711 (m-10) REVERT: H 93 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: K 366 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8450 (tp30) REVERT: K 370 ASP cc_start: 0.8528 (m-30) cc_final: 0.7933 (m-30) REVERT: K 561 MET cc_start: 0.8970 (mpp) cc_final: 0.8646 (mpp) outliers start: 12 outliers final: 5 residues processed: 188 average time/residue: 0.2718 time to fit residues: 75.3525 Evaluate side-chains 166 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 118 VAL 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 375 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 63 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 = 0.3844 r_free = 0.3844 target = 0.097888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.063107 restraints weight = 45069.056| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.52 r_work: 0.2837 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1727 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= 0.176 Angle : 0.538 6.050 22722 Z= 0.317 Chirality : 0.034 0.142 2510 Planarity : 0.004 0.053 1918 Dihedral : 29.130 171.595 4521 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.02 % Allowed : 12.99 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.25), residues: 1179 helix: 2.48 (0.18), residues: 824 sheet: -2.01 (1.40), residues: 16 loop : -0.73 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 220 HIS 0.005 0.001 HIS B 75 PHE 0.007 0.001 PHE K 186 TYR 0.014 0.001 TYR D 40 ARG 0.007 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 959) hydrogen bonds : angle 3.10811 ( 2498) covalent geometry : bond 0.00389 (15912) covalent geometry : angle 0.53793 (22722) *********************** 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 195 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9318 (m-10) cc_final: 0.9023 (m-80) REVERT: C 35 ARG cc_start: 0.9301 (tpp80) cc_final: 0.8879 (tpp80) REVERT: C 73 ASN cc_start: 0.9127 (t0) cc_final: 0.8655 (t0) REVERT: C 90 ASP cc_start: 0.8522 (t0) cc_final: 0.8303 (t0) REVERT: D 62 MET cc_start: 0.9253 (mmt) cc_final: 0.8932 (mmt) REVERT: D 68 ASP cc_start: 0.9305 (t0) cc_final: 0.8924 (t0) REVERT: D 93 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8536 (mt-10) REVERT: E 76 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8674 (tm-30) REVERT: E 90 MET cc_start: 0.8856 (mmp) cc_final: 0.8612 (mmt) REVERT: F 88 TYR cc_start: 0.8983 (m-10) cc_final: 0.8516 (m-10) REVERT: F 96 THR cc_start: 0.9554 (m) cc_final: 0.9319 (p) REVERT: G 90 ASP cc_start: 0.8448 (t0) cc_final: 0.8058 (t0) REVERT: H 71 GLU cc_start: 0.8889 (tp30) cc_final: 0.8677 (tm-30) REVERT: H 83 TYR cc_start: 0.8086 (m-10) cc_final: 0.7686 (m-10) REVERT: H 93 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: K 264 LEU cc_start: 0.9659 (mt) cc_final: 0.9395 (mt) REVERT: K 366 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8435 (tp30) REVERT: K 370 ASP cc_start: 0.8520 (m-30) cc_final: 0.7886 (m-30) REVERT: K 424 GLU cc_start: 0.9049 (tt0) cc_final: 0.8828 (tt0) REVERT: K 561 MET cc_start: 0.8949 (mpp) cc_final: 0.8608 (mpp) outliers start: 18 outliers final: 6 residues processed: 188 average time/residue: 0.2676 time to fit residues: 73.1938 Evaluate side-chains 174 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 372 ILE 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 135 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.098748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.065038 restraints weight = 44310.103| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.46 r_work: 0.2877 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2044 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= 0.141 Angle : 0.530 10.431 22722 Z= 0.310 Chirality : 0.033 0.143 2510 Planarity : 0.004 0.056 1918 Dihedral : 29.008 171.040 4518 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.57 % Allowed : 15.01 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.25), residues: 1179 helix: 2.62 (0.18), residues: 825 sheet: -1.98 (1.42), residues: 16 loop : -0.62 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 220 HIS 0.004 0.000 HIS B 75 PHE 0.019 0.001 PHE K 186 TYR 0.011 0.001 TYR D 40 ARG 0.007 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 959) hydrogen bonds : angle 2.93746 ( 2498) covalent geometry : bond 0.00302 (15912) covalent geometry : angle 0.53009 (22722) *********************** 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 196 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9302 (m-10) cc_final: 0.8996 (m-80) REVERT: C 35 ARG cc_start: 0.9278 (tpp80) cc_final: 0.8811 (tpp80) REVERT: C 73 ASN cc_start: 0.9149 (t0) cc_final: 0.8674 (t0) REVERT: C 90 ASP cc_start: 0.8475 (t0) cc_final: 0.8146 (t0) REVERT: C 110 ASN cc_start: 0.8357 (t0) cc_final: 0.7396 (p0) REVERT: E 51 ILE cc_start: 0.8400 (mt) cc_final: 0.8102 (mp) REVERT: E 76 GLN cc_start: 0.9041 (tm-30) cc_final: 0.8678 (tm-30) REVERT: E 90 MET cc_start: 0.8845 (mmp) cc_final: 0.8614 (mmt) REVERT: F 84 MET cc_start: 0.8700 (mmm) cc_final: 0.8362 (mmm) REVERT: F 88 TYR cc_start: 0.8979 (m-10) cc_final: 0.8415 (m-10) REVERT: F 96 THR cc_start: 0.9541 (m) cc_final: 0.9317 (p) REVERT: G 90 ASP cc_start: 0.8385 (t0) cc_final: 0.8055 (t70) REVERT: H 71 GLU cc_start: 0.8915 (tp30) cc_final: 0.8687 (tm-30) REVERT: H 93 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8163 (mp0) REVERT: K 336 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8313 (pm20) REVERT: K 366 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8497 (tp30) REVERT: K 370 ASP cc_start: 0.8549 (m-30) cc_final: 0.7907 (m-30) REVERT: K 424 GLU cc_start: 0.9023 (tt0) cc_final: 0.8766 (tt0) REVERT: K 561 MET cc_start: 0.8910 (mpp) cc_final: 0.8558 (mpp) outliers start: 14 outliers final: 6 residues processed: 193 average time/residue: 0.2779 time to fit residues: 77.8980 Evaluate side-chains 175 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 166 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 336 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 74 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 17 optimal weight: 0.0270 chunk 79 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 114 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.098942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.065271 restraints weight = 45388.478| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.50 r_work: 0.2893 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15912 Z= 0.140 Angle : 0.531 11.787 22722 Z= 0.308 Chirality : 0.033 0.142 2510 Planarity : 0.004 0.057 1918 Dihedral : 28.941 170.232 4518 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.68 % Allowed : 16.24 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.25), residues: 1179 helix: 2.69 (0.18), residues: 825 sheet: -1.91 (1.45), residues: 16 loop : -0.46 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 220 HIS 0.004 0.001 HIS B 75 PHE 0.007 0.001 PHE K 186 TYR 0.010 0.001 TYR D 40 ARG 0.009 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 959) hydrogen bonds : angle 2.86240 ( 2498) covalent geometry : bond 0.00303 (15912) covalent geometry : angle 0.53142 (22722) *********************** 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 198 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9274 (m-10) cc_final: 0.9014 (m-80) REVERT: C 35 ARG cc_start: 0.9267 (tpp80) cc_final: 0.8806 (tpp80) REVERT: C 73 ASN cc_start: 0.9166 (t0) cc_final: 0.8717 (t0) REVERT: C 90 ASP cc_start: 0.8479 (t0) cc_final: 0.8131 (t0) REVERT: C 110 ASN cc_start: 0.8436 (t0) cc_final: 0.7591 (p0) REVERT: E 76 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8695 (tm-30) REVERT: E 90 MET cc_start: 0.8835 (mmp) cc_final: 0.8500 (mmt) REVERT: G 90 ASP cc_start: 0.8382 (t0) cc_final: 0.8041 (t70) REVERT: H 71 GLU cc_start: 0.8916 (tp30) cc_final: 0.8665 (tm-30) REVERT: H 83 TYR cc_start: 0.8206 (m-10) cc_final: 0.7856 (m-10) REVERT: H 93 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: K 278 MET cc_start: 0.7977 (ttt) cc_final: 0.7506 (tmm) REVERT: K 280 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9215 (mp) REVERT: K 366 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8503 (tp30) REVERT: K 370 ASP cc_start: 0.8502 (m-30) cc_final: 0.7862 (m-30) REVERT: K 424 GLU cc_start: 0.8976 (tt0) cc_final: 0.8697 (tt0) REVERT: K 561 MET cc_start: 0.8868 (mpp) cc_final: 0.8513 (mpp) outliers start: 15 outliers final: 8 residues processed: 195 average time/residue: 0.2901 time to fit residues: 81.7691 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 : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain K residue 177 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 141 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 117 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 = 0.098324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.063442 restraints weight = 45328.526| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.55 r_work: 0.2853 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2343 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= 0.180 Angle : 0.544 9.350 22722 Z= 0.315 Chirality : 0.034 0.162 2510 Planarity : 0.004 0.055 1918 Dihedral : 29.037 170.417 4518 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.35 % Allowed : 16.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.25), residues: 1179 helix: 2.67 (0.18), residues: 826 sheet: -1.74 (1.46), residues: 16 loop : -0.37 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 220 HIS 0.006 0.001 HIS B 75 PHE 0.019 0.001 PHE K 186 TYR 0.011 0.001 TYR G 57 ARG 0.008 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 959) hydrogen bonds : angle 2.96132 ( 2498) covalent geometry : bond 0.00403 (15912) covalent geometry : angle 0.54444 (22722) *********************** 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 191 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9306 (m-10) cc_final: 0.8929 (m-80) REVERT: C 73 ASN cc_start: 0.9158 (t0) cc_final: 0.8694 (t0) REVERT: C 90 ASP cc_start: 0.8461 (t0) cc_final: 0.8107 (t0) REVERT: C 110 ASN cc_start: 0.8428 (t0) cc_final: 0.7641 (p0) REVERT: E 76 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8711 (tm-30) REVERT: E 90 MET cc_start: 0.8814 (mmp) cc_final: 0.8564 (mmt) REVERT: G 61 GLU cc_start: 0.8531 (tp30) cc_final: 0.8296 (tm-30) REVERT: G 90 ASP cc_start: 0.8512 (t0) cc_final: 0.8131 (t70) REVERT: H 71 GLU cc_start: 0.8962 (tp30) cc_final: 0.8730 (tm-30) REVERT: H 83 TYR cc_start: 0.7972 (m-10) cc_final: 0.7764 (m-10) REVERT: H 93 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8183 (mp0) REVERT: K 278 MET cc_start: 0.8055 (ttt) cc_final: 0.7602 (tmm) REVERT: K 280 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9258 (mp) REVERT: K 366 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8539 (tp30) REVERT: K 370 ASP cc_start: 0.8542 (m-30) cc_final: 0.7914 (m-30) REVERT: K 424 GLU cc_start: 0.9026 (tt0) cc_final: 0.8775 (tt0) REVERT: K 561 MET cc_start: 0.8916 (mpp) cc_final: 0.8613 (mpp) outliers start: 21 outliers final: 15 residues processed: 185 average time/residue: 0.2686 time to fit residues: 72.7075 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 : 1.134 ------------------------------------------------------------------------------- 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 D residue 89 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 96 THR 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 177 LEU 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 375 LEU 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 143 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.098848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.065187 restraints weight = 45109.602| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.50 r_work: 0.2892 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15912 Z= 0.145 Angle : 0.543 10.218 22722 Z= 0.312 Chirality : 0.033 0.188 2510 Planarity : 0.004 0.057 1918 Dihedral : 28.936 169.734 4518 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.02 % Allowed : 17.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.25), residues: 1179 helix: 2.70 (0.18), residues: 827 sheet: -1.68 (1.46), residues: 16 loop : -0.23 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 220 HIS 0.004 0.001 HIS B 75 PHE 0.006 0.001 PHE E 67 TYR 0.010 0.001 TYR C 50 ARG 0.008 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 959) hydrogen bonds : angle 2.87071 ( 2498) covalent geometry : bond 0.00317 (15912) covalent geometry : angle 0.54328 (22722) *********************** 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 194 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9270 (m-10) cc_final: 0.8867 (m-80) REVERT: C 73 ASN cc_start: 0.9189 (t0) cc_final: 0.8752 (t0) REVERT: C 90 ASP cc_start: 0.8488 (t0) cc_final: 0.8114 (t0) REVERT: C 110 ASN cc_start: 0.8384 (t0) cc_final: 0.7653 (p0) REVERT: D 79 ARG cc_start: 0.8588 (mtp85) cc_final: 0.8372 (mtp85) REVERT: E 50 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8294 (mt-10) REVERT: E 51 ILE cc_start: 0.8419 (mt) cc_final: 0.8159 (mp) REVERT: E 76 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8700 (tm-30) REVERT: G 61 GLU cc_start: 0.8491 (tp30) cc_final: 0.8283 (tm-30) REVERT: G 90 ASP cc_start: 0.8566 (t0) cc_final: 0.7694 (t70) REVERT: H 46 LYS cc_start: 0.9387 (mmmt) cc_final: 0.9037 (mmmm) REVERT: H 68 ASP cc_start: 0.9145 (t0) cc_final: 0.8939 (t0) REVERT: H 71 GLU cc_start: 0.8939 (tp30) cc_final: 0.8722 (tm-30) REVERT: H 83 TYR cc_start: 0.7874 (m-10) cc_final: 0.7619 (m-10) REVERT: H 93 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8243 (mp0) REVERT: K 260 GLN cc_start: 0.9554 (tt0) cc_final: 0.9108 (tp40) REVERT: K 278 MET cc_start: 0.8043 (ttt) cc_final: 0.7589 (tmm) REVERT: K 280 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9116 (mp) REVERT: K 366 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8515 (tp30) REVERT: K 370 ASP cc_start: 0.8534 (m-30) cc_final: 0.7882 (m-30) REVERT: K 424 GLU cc_start: 0.8998 (tt0) cc_final: 0.8712 (tt0) REVERT: K 561 MET cc_start: 0.8877 (mpp) cc_final: 0.8544 (mpp) outliers start: 18 outliers final: 11 residues processed: 190 average time/residue: 0.2644 time to fit residues: 74.7233 Evaluate side-chains 186 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 118 VAL 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 177 LEU 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 111 optimal weight: 50.0000 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 127 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.097798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.063995 restraints weight = 44721.733| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.45 r_work: 0.2859 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2508 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= 0.194 Angle : 0.571 9.496 22722 Z= 0.325 Chirality : 0.035 0.192 2510 Planarity : 0.004 0.055 1918 Dihedral : 29.066 169.888 4518 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.24 % Allowed : 17.58 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.25), residues: 1179 helix: 2.63 (0.18), residues: 827 sheet: -1.63 (1.47), residues: 16 loop : -0.24 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 220 HIS 0.005 0.001 HIS B 75 PHE 0.021 0.001 PHE K 186 TYR 0.012 0.001 TYR C 50 ARG 0.009 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 959) hydrogen bonds : angle 2.98362 ( 2498) covalent geometry : bond 0.00438 (15912) covalent geometry : angle 0.57059 (22722) *********************** 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 188 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.292 Fit side-chains REVERT: B 88 TYR cc_start: 0.9340 (m-10) cc_final: 0.8969 (m-80) REVERT: C 73 ASN cc_start: 0.9183 (t0) cc_final: 0.8754 (t0) REVERT: C 90 ASP cc_start: 0.8505 (t0) cc_final: 0.8137 (t0) REVERT: C 110 ASN cc_start: 0.8425 (t0) cc_final: 0.7737 (p0) REVERT: E 76 GLN cc_start: 0.9107 (tm-30) cc_final: 0.8703 (tm-30) REVERT: E 90 MET cc_start: 0.8930 (mmm) cc_final: 0.8701 (mmt) REVERT: G 61 GLU cc_start: 0.8575 (tp30) cc_final: 0.8279 (tm-30) REVERT: G 90 ASP cc_start: 0.8621 (t0) cc_final: 0.8280 (t0) REVERT: H 46 LYS cc_start: 0.9409 (mmmt) cc_final: 0.9060 (mmmm) REVERT: H 68 ASP cc_start: 0.9136 (t0) cc_final: 0.8882 (t0) REVERT: H 71 GLU cc_start: 0.8930 (tp30) cc_final: 0.8718 (tm-30) REVERT: H 83 TYR cc_start: 0.7850 (m-10) cc_final: 0.7627 (m-10) REVERT: H 93 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: K 260 GLN cc_start: 0.9474 (tt0) cc_final: 0.9177 (tp-100) REVERT: K 278 MET cc_start: 0.8150 (ttt) cc_final: 0.7679 (tmm) REVERT: K 280 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9103 (mp) REVERT: K 366 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8526 (tp30) REVERT: K 370 ASP cc_start: 0.8556 (m-30) cc_final: 0.7913 (m-30) REVERT: K 561 MET cc_start: 0.8925 (mpp) cc_final: 0.8629 (mpp) outliers start: 20 outliers final: 15 residues processed: 180 average time/residue: 0.2590 time to fit residues: 68.7603 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 : 1.145 ------------------------------------------------------------------------------- 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 D residue 89 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain F residue 96 THR 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 177 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 280 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 102 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.096707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.061896 restraints weight = 45209.734| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.52 r_work: 0.2812 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15912 Z= 0.253 Angle : 0.618 9.817 22722 Z= 0.348 Chirality : 0.037 0.242 2510 Planarity : 0.004 0.055 1918 Dihedral : 29.281 170.141 4518 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.88 % Favored : 97.03 % Rotamer: Outliers : 2.46 % Allowed : 17.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.25), residues: 1179 helix: 2.49 (0.18), residues: 827 sheet: -1.66 (1.46), residues: 16 loop : -0.36 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 220 HIS 0.006 0.001 HIS B 75 PHE 0.008 0.001 PHE C 25 TYR 0.015 0.001 TYR C 50 ARG 0.010 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 959) hydrogen bonds : angle 3.17211 ( 2498) covalent geometry : bond 0.00573 (15912) covalent geometry : angle 0.61766 (22722) *********************** 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 184 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 1.228 Fit side-chains REVERT: B 84 MET cc_start: 0.8948 (mmm) cc_final: 0.8526 (tmm) REVERT: C 73 ASN cc_start: 0.9125 (t0) cc_final: 0.8689 (t0) REVERT: C 90 ASP cc_start: 0.8517 (t0) cc_final: 0.8194 (t0) REVERT: C 110 ASN cc_start: 0.8465 (t0) cc_final: 0.7833 (p0) REVERT: E 76 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8898 (tm-30) REVERT: E 90 MET cc_start: 0.8953 (mmm) cc_final: 0.8741 (mmt) REVERT: G 61 GLU cc_start: 0.8676 (tp30) cc_final: 0.8198 (tp30) REVERT: G 90 ASP cc_start: 0.8706 (t0) cc_final: 0.8285 (t0) REVERT: H 46 LYS cc_start: 0.9416 (mmmt) cc_final: 0.9074 (mmmm) REVERT: H 68 ASP cc_start: 0.9172 (t0) cc_final: 0.8887 (t0) REVERT: H 83 TYR cc_start: 0.7901 (m-10) cc_final: 0.7622 (m-10) REVERT: H 93 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8266 (mp0) REVERT: K 239 MET cc_start: 0.9196 (ttt) cc_final: 0.8961 (ttm) REVERT: K 260 GLN cc_start: 0.9504 (tt0) cc_final: 0.9130 (tp-100) REVERT: K 278 MET cc_start: 0.8159 (ttt) cc_final: 0.7632 (tmm) REVERT: K 366 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8485 (tp30) REVERT: K 370 ASP cc_start: 0.8574 (m-30) cc_final: 0.7854 (m-30) REVERT: K 561 MET cc_start: 0.8957 (mpp) cc_final: 0.8663 (mpp) REVERT: K 571 ASN cc_start: 0.8851 (t0) cc_final: 0.8602 (t0) outliers start: 22 outliers final: 17 residues processed: 178 average time/residue: 0.2763 time to fit residues: 72.0746 Evaluate side-chains 178 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 89 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 96 THR 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 177 LEU Chi-restraints excluded: chain K residue 254 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 32 optimal weight: 2.9990 chunk 111 optimal weight: 50.0000 chunk 30 optimal weight: 0.8980 chunk 65 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.098450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.064748 restraints weight = 45156.230| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.51 r_work: 0.2881 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15912 Z= 0.146 Angle : 0.578 9.619 22722 Z= 0.327 Chirality : 0.034 0.219 2510 Planarity : 0.004 0.057 1918 Dihedral : 28.992 168.459 4518 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.46 % Favored : 97.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.25), residues: 1179 helix: 2.62 (0.18), residues: 828 sheet: -1.56 (1.49), residues: 16 loop : -0.22 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 220 HIS 0.005 0.001 HIS B 75 PHE 0.018 0.001 PHE K 186 TYR 0.012 0.001 TYR D 40 ARG 0.006 0.000 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 959) hydrogen bonds : angle 2.90163 ( 2498) covalent geometry : bond 0.00320 (15912) covalent geometry : angle 0.57765 (22722) ********************** 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 198 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 1.283 Fit side-chains REVERT: B 84 MET cc_start: 0.8814 (mmm) cc_final: 0.8316 (tmm) REVERT: C 73 ASN cc_start: 0.9155 (t0) cc_final: 0.8743 (t0) REVERT: C 90 ASP cc_start: 0.8502 (t0) cc_final: 0.8171 (t0) REVERT: C 110 ASN cc_start: 0.8433 (t0) cc_final: 0.7884 (p0) REVERT: D 83 TYR cc_start: 0.8725 (m-10) cc_final: 0.8208 (m-80) REVERT: E 76 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8689 (tm-30) REVERT: F 44 LYS cc_start: 0.9315 (mttp) cc_final: 0.9040 (mttt) REVERT: G 51 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9185 (tp) REVERT: G 61 GLU cc_start: 0.8495 (tp30) cc_final: 0.8257 (tm-30) REVERT: G 90 ASP cc_start: 0.8588 (t0) cc_final: 0.7757 (t0) REVERT: H 46 LYS cc_start: 0.9371 (mmmt) cc_final: 0.9068 (mmmm) REVERT: H 68 ASP cc_start: 0.9134 (t0) cc_final: 0.8891 (t0) REVERT: H 83 TYR cc_start: 0.7756 (m-10) cc_final: 0.7483 (m-10) REVERT: H 93 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: K 239 MET cc_start: 0.9259 (ttt) cc_final: 0.9026 (ttm) REVERT: K 260 GLN cc_start: 0.9503 (tt0) cc_final: 0.9213 (tp-100) REVERT: K 278 MET cc_start: 0.8165 (ttt) cc_final: 0.7631 (tmm) REVERT: K 366 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8542 (tp30) REVERT: K 370 ASP cc_start: 0.8552 (m-30) cc_final: 0.7913 (m-30) outliers start: 18 outliers final: 13 residues processed: 194 average time/residue: 0.2770 time to fit residues: 79.2621 Evaluate side-chains 189 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 118 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 236 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 61 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 108 optimal weight: 50.0000 chunk 143 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.098575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.064129 restraints weight = 44919.755| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.51 r_work: 0.2881 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2758 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= 0.153 Angle : 0.576 10.031 22722 Z= 0.326 Chirality : 0.034 0.214 2510 Planarity : 0.004 0.056 1918 Dihedral : 29.002 168.476 4518 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.54 % Rotamer: Outliers : 1.90 % Allowed : 17.92 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.25), residues: 1179 helix: 2.61 (0.18), residues: 828 sheet: -1.55 (1.49), residues: 16 loop : -0.20 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 220 HIS 0.004 0.001 HIS B 75 PHE 0.007 0.001 PHE K 238 TYR 0.012 0.001 TYR C 50 ARG 0.010 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 959) hydrogen bonds : angle 2.92464 ( 2498) covalent geometry : bond 0.00339 (15912) covalent geometry : angle 0.57600 (22722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7476.78 seconds wall clock time: 129 minutes 36.73 seconds (7776.73 seconds total)