Starting phenix.real_space_refine on Fri Jun 13 05:16:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gpn_34195/06_2025/8gpn_34195.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gpn_34195/06_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_34195/06_2025/8gpn_34195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gpn_34195/06_2025/8gpn_34195.map" model { file = "/net/cci-nas-00/data/ceres_data/8gpn_34195/06_2025/8gpn_34195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gpn_34195/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.95, per 1000 atoms: 0.59 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: 4.56 Conformation dependent library (CDL) restraints added in 1.8 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: 8.20 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: 7.56 Time building geometry restraints manager: 4.95 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: 1.070 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: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 44.670 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.070 ------------------------------------------------------------------------------- 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 : 1.224 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 200 average time/residue: 0.3152 time to fit residues: 88.2245 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 : 1.212 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.098350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.063570 restraints weight = 44470.311| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.47 r_work: 0.2854 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15912 Z= 0.162 Angle : 0.556 6.829 22722 Z= 0.327 Chirality : 0.035 0.148 2510 Planarity : 0.004 0.057 1918 Dihedral : 29.283 172.320 4521 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.46 % Allowed : 11.98 % 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 0.015 0.001 TYR B 88 ARG 0.007 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 959) hydrogen bonds : angle 3.26331 ( 2498) covalent geometry : bond 0.00354 (15912) covalent geometry : angle 0.55569 (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 194 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 THR cc_start: 0.9562 (OUTLIER) cc_final: 0.9345 (p) REVERT: B 88 TYR cc_start: 0.9251 (m-80) cc_final: 0.8979 (m-10) REVERT: C 35 ARG cc_start: 0.9252 (tpp80) cc_final: 0.8834 (tpp80) REVERT: C 73 ASN cc_start: 0.9091 (t0) cc_final: 0.8644 (t0) REVERT: D 62 MET cc_start: 0.9282 (mmt) cc_final: 0.9021 (mmt) REVERT: D 68 ASP cc_start: 0.9277 (t0) cc_final: 0.8995 (t0) REVERT: D 106 LEU cc_start: 0.9254 (mt) cc_final: 0.9037 (mt) REVERT: E 90 MET cc_start: 0.8849 (mmp) cc_final: 0.8589 (mmt) REVERT: E 123 ASP cc_start: 0.9043 (m-30) cc_final: 0.8843 (m-30) REVERT: F 88 TYR cc_start: 0.8890 (m-10) cc_final: 0.8626 (m-10) REVERT: F 93 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8974 (mm-40) REVERT: G 90 ASP cc_start: 0.8331 (t0) cc_final: 0.8117 (t0) REVERT: H 83 TYR cc_start: 0.8011 (m-10) cc_final: 0.7702 (m-10) REVERT: H 93 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8266 (mp0) REVERT: K 366 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8441 (tp30) REVERT: K 370 ASP cc_start: 0.8560 (m-30) cc_final: 0.7954 (m-30) REVERT: K 561 MET cc_start: 0.8979 (mpp) cc_final: 0.8641 (mpp) outliers start: 13 outliers final: 5 residues processed: 188 average time/residue: 0.2680 time to fit residues: 74.0076 Evaluate side-chains 168 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 46 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.097858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.063749 restraints weight = 44583.505| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.49 r_work: 0.2849 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1710 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= 0.167 Angle : 0.535 6.278 22722 Z= 0.316 Chirality : 0.034 0.143 2510 Planarity : 0.004 0.053 1918 Dihedral : 29.116 171.600 4521 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.57 % Allowed : 13.10 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.29 (0.25), residues: 1179 helix: 2.46 (0.18), residues: 824 sheet: -2.03 (1.40), residues: 16 loop : -0.74 (0.33), residues: 339 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 0.007 0.001 PHE K 186 TYR 0.011 0.001 TYR D 40 ARG 0.006 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 959) hydrogen bonds : angle 3.10349 ( 2498) covalent geometry : bond 0.00367 (15912) covalent geometry : angle 0.53457 (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 191 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9285 (m-10) cc_final: 0.9005 (m-80) REVERT: C 35 ARG cc_start: 0.9294 (tpp80) cc_final: 0.8861 (tpp80) REVERT: C 73 ASN cc_start: 0.9123 (t0) cc_final: 0.8649 (t0) REVERT: D 62 MET cc_start: 0.9277 (mmt) cc_final: 0.8944 (mmt) REVERT: D 93 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8567 (mt-10) REVERT: E 76 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8657 (tm-30) REVERT: E 90 MET cc_start: 0.8877 (mmp) cc_final: 0.8626 (mmt) REVERT: F 88 TYR cc_start: 0.8958 (m-10) cc_final: 0.8526 (m-10) REVERT: F 96 THR cc_start: 0.9559 (m) cc_final: 0.9298 (p) REVERT: G 90 ASP cc_start: 0.8422 (t0) cc_final: 0.8124 (t70) REVERT: H 71 GLU cc_start: 0.8895 (tp30) cc_final: 0.8679 (tm-30) REVERT: H 83 TYR cc_start: 0.8043 (m-10) cc_final: 0.7671 (m-10) REVERT: H 93 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8210 (mp0) REVERT: K 366 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8419 (tp30) REVERT: K 370 ASP cc_start: 0.8570 (m-30) cc_final: 0.7884 (m-30) REVERT: K 424 GLU cc_start: 0.9056 (tt0) cc_final: 0.8831 (tt0) REVERT: K 561 MET cc_start: 0.8942 (mpp) cc_final: 0.8574 (mpp) outliers start: 14 outliers final: 4 residues processed: 187 average time/residue: 0.3203 time to fit residues: 87.6133 Evaluate side-chains 172 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 372 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.099071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.065256 restraints weight = 44317.373| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.48 r_work: 0.2887 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2116 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= 0.139 Angle : 0.530 10.784 22722 Z= 0.309 Chirality : 0.033 0.143 2510 Planarity : 0.004 0.056 1918 Dihedral : 28.956 170.827 4518 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.34 % Allowed : 14.56 % Favored : 84.10 % 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: 2.56 (0.25), residues: 1179 helix: 2.64 (0.18), residues: 825 sheet: -1.97 (1.44), residues: 16 loop : -0.57 (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 F 88 ARG 0.008 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 959) hydrogen bonds : angle 2.88962 ( 2498) covalent geometry : bond 0.00297 (15912) covalent geometry : angle 0.53019 (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 201 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 189 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9273 (m-10) cc_final: 0.8914 (m-10) REVERT: C 35 ARG cc_start: 0.9271 (tpp80) cc_final: 0.8813 (tpp80) REVERT: C 73 ASN cc_start: 0.9159 (t0) cc_final: 0.8683 (t0) REVERT: C 110 ASN cc_start: 0.8362 (t0) cc_final: 0.7418 (p0) REVERT: E 51 ILE cc_start: 0.8433 (mt) cc_final: 0.8144 (mp) REVERT: E 76 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8696 (tm-30) REVERT: E 90 MET cc_start: 0.8869 (mmp) cc_final: 0.8627 (mmt) REVERT: F 84 MET cc_start: 0.8698 (mmm) cc_final: 0.8392 (mmm) REVERT: F 88 TYR cc_start: 0.8991 (m-10) cc_final: 0.8392 (m-10) REVERT: F 96 THR cc_start: 0.9529 (m) cc_final: 0.9320 (p) REVERT: G 90 ASP cc_start: 0.8381 (t0) cc_final: 0.8067 (t70) REVERT: H 71 GLU cc_start: 0.8862 (tp30) cc_final: 0.8640 (tm-30) REVERT: H 93 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8193 (mp0) REVERT: K 260 GLN cc_start: 0.9528 (tt0) cc_final: 0.9155 (tp40) REVERT: K 336 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8322 (pm20) REVERT: K 366 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8494 (tp30) REVERT: K 370 ASP cc_start: 0.8527 (m-30) cc_final: 0.7878 (m-30) REVERT: K 424 GLU cc_start: 0.9000 (tt0) cc_final: 0.8744 (tt0) REVERT: K 561 MET cc_start: 0.8889 (mpp) cc_final: 0.8535 (mpp) outliers start: 12 outliers final: 6 residues processed: 199 average time/residue: 0.3194 time to fit residues: 93.1597 Evaluate side-chains 180 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 171 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 30 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 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: 0.6980 chunk 61 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 9 optimal weight: 0.0870 chunk 91 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 116 optimal weight: 0.0670 chunk 114 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.5700 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.098544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.064006 restraints weight = 45615.040| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.49 r_work: 0.2868 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2236 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= 0.165 Angle : 0.545 11.079 22722 Z= 0.314 Chirality : 0.034 0.141 2510 Planarity : 0.004 0.056 1918 Dihedral : 29.009 170.458 4518 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.79 % Allowed : 16.13 % 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: 2.63 (0.25), residues: 1179 helix: 2.68 (0.18), residues: 825 sheet: -1.92 (1.46), residues: 16 loop : -0.50 (0.33), residues: 338 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 0.006 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 0.03481 ( 959) hydrogen bonds : angle 2.93331 ( 2498) covalent geometry : bond 0.00366 (15912) covalent geometry : angle 0.54475 (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 191 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9283 (m-10) cc_final: 0.8971 (m-80) REVERT: C 35 ARG cc_start: 0.9281 (tpp80) cc_final: 0.8814 (tpp80) REVERT: C 73 ASN cc_start: 0.9152 (t0) cc_final: 0.8688 (t0) REVERT: C 110 ASN cc_start: 0.8429 (t0) cc_final: 0.7578 (p0) REVERT: D 33 ARG cc_start: 0.7686 (ttm-80) cc_final: 0.7120 (ttm-80) REVERT: E 76 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8696 (tm-30) REVERT: E 90 MET cc_start: 0.8877 (mmp) cc_final: 0.8659 (mmt) REVERT: F 84 MET cc_start: 0.8591 (mmm) cc_final: 0.8242 (mmm) REVERT: G 90 ASP cc_start: 0.8416 (t0) cc_final: 0.8078 (t70) REVERT: H 71 GLU cc_start: 0.8916 (tp30) cc_final: 0.8680 (tm-30) REVERT: H 83 TYR cc_start: 0.8241 (m-10) cc_final: 0.8022 (m-10) REVERT: H 93 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: K 280 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9223 (mp) REVERT: K 366 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8520 (tp30) REVERT: K 370 ASP cc_start: 0.8501 (m-30) cc_final: 0.7866 (m-30) REVERT: K 424 GLU cc_start: 0.9001 (tt0) cc_final: 0.8751 (tt0) REVERT: K 561 MET cc_start: 0.8874 (mpp) cc_final: 0.8561 (mpp) outliers start: 16 outliers final: 10 residues processed: 187 average time/residue: 0.3308 time to fit residues: 92.8042 Evaluate side-chains 178 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 chunk 59 optimal weight: 0.0070 chunk 6 optimal weight: 4.9990 chunk 117 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.097323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.062474 restraints weight = 45363.707| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.52 r_work: 0.2827 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2216 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= 0.218 Angle : 0.570 8.288 22722 Z= 0.327 Chirality : 0.036 0.151 2510 Planarity : 0.004 0.055 1918 Dihedral : 29.154 170.705 4518 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.24 % Allowed : 16.46 % 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: 2.56 (0.25), residues: 1179 helix: 2.59 (0.18), residues: 827 sheet: -1.87 (1.43), residues: 16 loop : -0.45 (0.33), residues: 336 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 0.022 0.002 PHE K 186 TYR 0.012 0.001 TYR G 57 ARG 0.009 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 959) hydrogen bonds : angle 3.05916 ( 2498) covalent geometry : bond 0.00490 (15912) covalent geometry : angle 0.56960 (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 188 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.9353 (m-10) cc_final: 0.9019 (m-80) REVERT: C 73 ASN cc_start: 0.9128 (t0) cc_final: 0.8647 (t0) REVERT: C 110 ASN cc_start: 0.8423 (t0) cc_final: 0.7622 (p0) REVERT: E 76 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8719 (tm-30) REVERT: E 90 MET cc_start: 0.8898 (mmp) cc_final: 0.8673 (mmt) REVERT: F 84 MET cc_start: 0.8742 (mmm) cc_final: 0.8436 (mmm) REVERT: G 90 ASP cc_start: 0.8534 (t0) cc_final: 0.8245 (t0) REVERT: H 71 GLU cc_start: 0.8951 (tp30) cc_final: 0.8744 (tm-30) REVERT: H 93 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8205 (mp0) REVERT: K 278 MET cc_start: 0.7981 (ttt) cc_final: 0.7529 (tmm) REVERT: K 280 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9289 (mp) REVERT: K 366 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8563 (tp30) REVERT: K 370 ASP cc_start: 0.8550 (m-30) cc_final: 0.7920 (m-30) REVERT: K 424 GLU cc_start: 0.9095 (tt0) cc_final: 0.8857 (tt0) REVERT: K 561 MET cc_start: 0.8936 (mpp) cc_final: 0.8632 (mpp) outliers start: 20 outliers final: 12 residues processed: 183 average time/residue: 0.2794 time to fit residues: 75.1727 Evaluate side-chains 176 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 1.412 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 143 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 30.0000 chunk 5 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.097903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.063384 restraints weight = 45161.851| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.50 r_work: 0.2854 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15912 Z= 0.172 Angle : 0.556 9.053 22722 Z= 0.320 Chirality : 0.034 0.188 2510 Planarity : 0.004 0.056 1918 Dihedral : 29.081 170.127 4518 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.02 % Allowed : 16.46 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.62 (0.25), residues: 1179 helix: 2.63 (0.18), residues: 827 sheet: -1.83 (1.46), residues: 16 loop : -0.40 (0.33), 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 0.006 0.001 PHE E 67 TYR 0.016 0.001 TYR H 83 ARG 0.008 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 959) hydrogen bonds : angle 2.98291 ( 2498) covalent geometry : bond 0.00384 (15912) covalent geometry : angle 0.55600 (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 191 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8849 (mmm) cc_final: 0.8176 (tmm) REVERT: C 73 ASN cc_start: 0.9132 (t0) cc_final: 0.8656 (t0) REVERT: C 110 ASN cc_start: 0.8425 (t0) cc_final: 0.7716 (p0) REVERT: E 76 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8716 (tm-30) REVERT: E 90 MET cc_start: 0.8877 (mmp) cc_final: 0.8571 (mmt) REVERT: G 90 ASP cc_start: 0.8532 (t0) cc_final: 0.7854 (t70) REVERT: H 68 ASP cc_start: 0.9151 (t0) cc_final: 0.8938 (t0) REVERT: H 71 GLU cc_start: 0.8889 (tp30) cc_final: 0.8683 (tm-30) REVERT: H 93 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8212 (mp0) REVERT: K 239 MET cc_start: 0.9240 (ttt) cc_final: 0.8908 (ttm) REVERT: K 260 GLN cc_start: 0.9518 (tt0) cc_final: 0.9106 (tp40) REVERT: K 278 MET cc_start: 0.8065 (ttt) cc_final: 0.7192 (tmm) REVERT: K 280 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9122 (mp) REVERT: K 282 ASN cc_start: 0.9308 (m-40) cc_final: 0.8250 (m-40) REVERT: K 366 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8546 (tp30) REVERT: K 370 ASP cc_start: 0.8488 (m-30) cc_final: 0.7842 (m-30) REVERT: K 561 MET cc_start: 0.8878 (mpp) cc_final: 0.8600 (mpp) outliers start: 18 outliers final: 13 residues processed: 185 average time/residue: 0.2785 time to fit residues: 75.2756 Evaluate side-chains 184 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 118 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 49 LEU 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: 6.9990 chunk 61 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 110 optimal weight: 0.0020 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.096264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.062327 restraints weight = 44981.899| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.46 r_work: 0.2815 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15912 Z= 0.266 Angle : 0.607 7.455 22722 Z= 0.347 Chirality : 0.037 0.193 2510 Planarity : 0.004 0.055 1918 Dihedral : 29.279 170.352 4518 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.13 % Allowed : 16.91 % Favored : 80.96 % 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: 2.41 (0.25), residues: 1179 helix: 2.47 (0.18), residues: 826 sheet: -1.85 (1.42), residues: 16 loop : -0.47 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 220 HIS 0.006 0.001 HIS B 75 PHE 0.021 0.002 PHE K 186 TYR 0.018 0.002 TYR F 88 ARG 0.009 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 959) hydrogen bonds : angle 3.20438 ( 2498) covalent geometry : bond 0.00603 (15912) covalent geometry : angle 0.60698 (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 177 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9092 (t0) cc_final: 0.8617 (t0) REVERT: C 110 ASN cc_start: 0.8485 (t0) cc_final: 0.7762 (p0) REVERT: E 76 GLN cc_start: 0.9193 (tm-30) cc_final: 0.8727 (tm-30) REVERT: E 90 MET cc_start: 0.8820 (mmp) cc_final: 0.8586 (mmt) REVERT: F 84 MET cc_start: 0.8793 (mmm) cc_final: 0.8531 (mmm) REVERT: G 61 GLU cc_start: 0.8601 (tp30) cc_final: 0.8242 (tp30) REVERT: G 90 ASP cc_start: 0.8670 (t0) cc_final: 0.8383 (t0) REVERT: H 68 ASP cc_start: 0.9181 (t0) cc_final: 0.8890 (t0) REVERT: H 93 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8229 (mp0) REVERT: K 260 GLN cc_start: 0.9495 (tt0) cc_final: 0.9211 (tp-100) REVERT: K 278 MET cc_start: 0.8103 (ttt) cc_final: 0.7234 (tmm) REVERT: K 282 ASN cc_start: 0.9346 (m-40) cc_final: 0.8362 (m-40) REVERT: K 366 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8470 (tp30) REVERT: K 370 ASP cc_start: 0.8577 (m-30) cc_final: 0.7861 (m-30) REVERT: K 561 MET cc_start: 0.8968 (mpp) cc_final: 0.8666 (mpp) REVERT: K 571 ASN cc_start: 0.8897 (t0) cc_final: 0.8621 (t0) outliers start: 19 outliers final: 16 residues processed: 171 average time/residue: 0.2761 time to fit residues: 69.2003 Evaluate side-chains 176 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 79 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 = 0.097172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.062696 restraints weight = 44989.803| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.45 r_work: 0.2836 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2457 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= 0.190 Angle : 0.578 8.457 22722 Z= 0.331 Chirality : 0.035 0.222 2510 Planarity : 0.004 0.056 1918 Dihedral : 29.170 169.547 4518 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.54 % Rotamer: Outliers : 2.35 % Allowed : 17.25 % 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: 2.47 (0.25), residues: 1179 helix: 2.49 (0.18), residues: 828 sheet: -1.88 (1.43), residues: 16 loop : -0.42 (0.34), residues: 335 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 0.006 0.001 PHE K 439 TYR 0.019 0.001 TYR F 88 ARG 0.009 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 959) hydrogen bonds : angle 3.05353 ( 2498) covalent geometry : bond 0.00428 (15912) covalent geometry : angle 0.57761 (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 190 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8831 (mmm) cc_final: 0.8332 (tmm) REVERT: C 35 ARG cc_start: 0.9294 (tpp80) cc_final: 0.8763 (tpp80) REVERT: C 73 ASN cc_start: 0.9101 (t0) cc_final: 0.8626 (t0) REVERT: C 110 ASN cc_start: 0.8450 (t0) cc_final: 0.7814 (p0) REVERT: E 50 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8315 (mt-10) REVERT: E 76 GLN cc_start: 0.9150 (tm-30) cc_final: 0.8718 (tm-30) REVERT: E 90 MET cc_start: 0.8740 (mmp) cc_final: 0.8513 (mmt) REVERT: F 44 LYS cc_start: 0.9278 (mttp) cc_final: 0.8988 (mttt) REVERT: G 61 GLU cc_start: 0.8487 (tp30) cc_final: 0.8281 (tm-30) REVERT: G 90 ASP cc_start: 0.8589 (t0) cc_final: 0.7693 (t0) REVERT: H 46 LYS cc_start: 0.9409 (mmmt) cc_final: 0.9091 (mmmm) REVERT: H 68 ASP cc_start: 0.9147 (t0) cc_final: 0.8891 (t0) REVERT: H 93 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8238 (mp0) REVERT: K 239 MET cc_start: 0.9274 (ttt) cc_final: 0.8937 (ttm) REVERT: K 260 GLN cc_start: 0.9506 (tt0) cc_final: 0.9149 (tp-100) REVERT: K 278 MET cc_start: 0.8067 (ttt) cc_final: 0.7176 (tmm) REVERT: K 280 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9141 (mp) REVERT: K 282 ASN cc_start: 0.9320 (m-40) cc_final: 0.8250 (m-40) REVERT: K 366 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8562 (tp30) REVERT: K 370 ASP cc_start: 0.8543 (m-30) cc_final: 0.7919 (m-30) REVERT: K 561 MET cc_start: 0.8908 (mpp) cc_final: 0.8620 (mpp) REVERT: K 571 ASN cc_start: 0.8908 (t0) cc_final: 0.8666 (t0) outliers start: 21 outliers final: 14 residues processed: 184 average time/residue: 0.2771 time to fit residues: 74.7653 Evaluate side-chains 183 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 49 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 579 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 32 optimal weight: 8.9990 chunk 111 optimal weight: 50.0000 chunk 30 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 34 optimal weight: 0.0770 chunk 125 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.098965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.065528 restraints weight = 45126.367| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.48 r_work: 0.2901 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2775 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= 0.140 Angle : 0.563 8.880 22722 Z= 0.323 Chirality : 0.034 0.206 2510 Planarity : 0.004 0.056 1918 Dihedral : 28.950 168.284 4518 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.54 % Rotamer: Outliers : 1.46 % Allowed : 18.37 % 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: 2.64 (0.25), residues: 1179 helix: 2.59 (0.18), residues: 828 sheet: -1.66 (1.46), residues: 16 loop : -0.25 (0.35), residues: 335 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 0.012 0.001 TYR D 42 ARG 0.009 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 959) hydrogen bonds : angle 2.89873 ( 2498) covalent geometry : bond 0.00305 (15912) covalent geometry : angle 0.56317 (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 195 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8800 (mmm) cc_final: 0.8326 (tmm) REVERT: C 73 ASN cc_start: 0.9179 (t0) cc_final: 0.8753 (t0) REVERT: C 110 ASN cc_start: 0.8443 (t0) cc_final: 0.7904 (p0) REVERT: E 76 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8690 (tm-30) REVERT: F 44 LYS cc_start: 0.9206 (mttp) cc_final: 0.8920 (mttt) REVERT: F 47 SER cc_start: 0.9283 (t) cc_final: 0.8823 (m) REVERT: F 88 TYR cc_start: 0.8236 (m-10) cc_final: 0.7688 (m-10) REVERT: G 90 ASP cc_start: 0.8496 (t0) cc_final: 0.7698 (t70) REVERT: H 46 LYS cc_start: 0.9399 (mmmt) cc_final: 0.9131 (mmmm) REVERT: H 68 ASP cc_start: 0.9155 (t0) cc_final: 0.8911 (t0) REVERT: H 83 TYR cc_start: 0.7530 (m-10) cc_final: 0.6933 (m-10) REVERT: H 93 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8239 (mp0) REVERT: K 239 MET cc_start: 0.9240 (ttt) cc_final: 0.8853 (ttm) REVERT: K 260 GLN cc_start: 0.9497 (tt0) cc_final: 0.9192 (tp-100) REVERT: K 278 MET cc_start: 0.8099 (ttt) cc_final: 0.7735 (tmm) REVERT: K 280 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9040 (mp) REVERT: K 366 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8537 (tp30) REVERT: K 370 ASP cc_start: 0.8524 (m-30) cc_final: 0.7912 (m-30) REVERT: K 571 ASN cc_start: 0.8886 (t0) cc_final: 0.8632 (t0) outliers start: 13 outliers final: 7 residues processed: 193 average time/residue: 0.2700 time to fit residues: 75.9186 Evaluate side-chains 180 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR 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 177 LEU Chi-restraints excluded: chain K residue 280 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 372 ILE Chi-restraints excluded: chain K residue 579 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 61 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 50.0000 chunk 143 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** H 84 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 = 0.3850 r_free = 0.3850 target = 0.097776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.064142 restraints weight = 44859.014| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.47 r_work: 0.2873 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2771 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= 0.176 Angle : 0.573 9.672 22722 Z= 0.327 Chirality : 0.034 0.213 2510 Planarity : 0.004 0.055 1918 Dihedral : 29.040 168.534 4518 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.12 % Favored : 97.79 % Rotamer: Outliers : 1.46 % Allowed : 18.48 % 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: 2.65 (0.25), residues: 1179 helix: 2.58 (0.18), residues: 828 sheet: -1.62 (1.47), residues: 16 loop : -0.20 (0.35), residues: 335 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 0.008 0.001 PHE K 238 TYR 0.016 0.001 TYR H 83 ARG 0.010 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 959) hydrogen bonds : angle 2.97108 ( 2498) covalent geometry : bond 0.00396 (15912) covalent geometry : angle 0.57279 (22722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7569.20 seconds wall clock time: 131 minutes 48.65 seconds (7908.65 seconds total)