Starting phenix.real_space_refine on Tue Dec 31 03:45:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gpn_34195/12_2024/8gpn_34195.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gpn_34195/12_2024/8gpn_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_34195/12_2024/8gpn_34195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gpn_34195/12_2024/8gpn_34195.map" model { file = "/net/cci-nas-00/data/ceres_data/8gpn_34195/12_2024/8gpn_34195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gpn_34195/12_2024/8gpn_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-5532/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: 8.84, 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: 3.96 Conformation dependent library (CDL) restraints added in 1.3 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: 7.46 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: 7.82 Time building geometry restraints manager: 4.50 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: 0.730 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: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 41.960 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.040 ------------------------------------------------------------------------------- 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= 0.401 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 *********************** 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 : 1.271 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 200 average time/residue: 0.3416 time to fit residues: 95.2262 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 : 1.566 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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= 0.204 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 *********************** 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 : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 35 ARG cc_start: 0.8209 (tpp80) cc_final: 0.7955 (tpp80) REVERT: F 93 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7804 (mm-40) outliers start: 12 outliers final: 5 residues processed: 188 average time/residue: 0.2870 time to fit residues: 79.5083 Evaluate side-chains 163 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 158 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 K residue 254 LEU 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 73 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 36 optimal weight: 30.0000 chunk 131 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15912 Z= 0.336 Angle : 0.587 6.113 22722 Z= 0.342 Chirality : 0.037 0.143 2510 Planarity : 0.004 0.052 1918 Dihedral : 29.330 172.099 4521 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.68 % Allowed : 13.66 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.25), residues: 1179 helix: 2.30 (0.18), residues: 826 sheet: -2.02 (1.41), residues: 16 loop : -0.79 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 220 HIS 0.006 0.001 HIS B 75 PHE 0.009 0.001 PHE C 25 TYR 0.027 0.002 TYR B 88 ARG 0.007 0.000 ARG D 86 *********************** 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 183 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 35 ARG cc_start: 0.8260 (tpp80) cc_final: 0.8017 (tpp80) REVERT: K 212 ASN cc_start: 0.7834 (p0) cc_final: 0.7558 (p0) outliers start: 15 outliers final: 7 residues processed: 179 average time/residue: 0.2967 time to fit residues: 77.3866 Evaluate side-chains 164 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 157 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain 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 130 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15912 Z= 0.269 Angle : 0.559 7.334 22722 Z= 0.328 Chirality : 0.035 0.144 2510 Planarity : 0.004 0.055 1918 Dihedral : 29.247 171.661 4521 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.46 % Allowed : 15.90 % Favored : 82.64 % 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: 2.32 (0.25), residues: 1179 helix: 2.46 (0.18), residues: 826 sheet: -2.04 (1.41), residues: 16 loop : -0.69 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 265 HIS 0.007 0.001 HIS B 75 PHE 0.019 0.001 PHE K 186 TYR 0.041 0.002 TYR B 88 ARG 0.008 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 1.289 Fit side-chains revert: symmetry clash REVERT: C 35 ARG cc_start: 0.8248 (tpp80) cc_final: 0.7983 (tpp80) REVERT: C 110 ASN cc_start: 0.7965 (t0) cc_final: 0.7457 (p0) REVERT: F 88 TYR cc_start: 0.7544 (m-10) cc_final: 0.6693 (m-10) REVERT: K 212 ASN cc_start: 0.7774 (p0) cc_final: 0.7549 (p0) outliers start: 13 outliers final: 9 residues processed: 179 average time/residue: 0.2942 time to fit residues: 76.4737 Evaluate side-chains 172 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 47 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 0.1980 chunk 79 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 104 optimal weight: 40.0000 chunk 57 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2081 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= 0.226 Angle : 0.545 7.444 22722 Z= 0.320 Chirality : 0.034 0.142 2510 Planarity : 0.004 0.055 1918 Dihedral : 29.157 170.661 4518 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.90 % Allowed : 16.24 % Favored : 81.86 % 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: 2.57 (0.18), residues: 826 sheet: -2.03 (1.42), residues: 16 loop : -0.57 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 265 HIS 0.005 0.001 HIS B 75 PHE 0.013 0.001 PHE K 238 TYR 0.038 0.001 TYR H 83 ARG 0.008 0.000 ARG D 86 *********************** 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 188 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 1.409 Fit side-chains revert: symmetry clash REVERT: C 35 ARG cc_start: 0.8253 (tpp80) cc_final: 0.7997 (tpp80) REVERT: C 110 ASN cc_start: 0.8044 (t0) cc_final: 0.7683 (p0) outliers start: 17 outliers final: 9 residues processed: 186 average time/residue: 0.2883 time to fit residues: 77.7988 Evaluate side-chains 171 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 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 K residue 254 LEU 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 47 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 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 D 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2190 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= 0.251 Angle : 0.563 11.017 22722 Z= 0.325 Chirality : 0.035 0.141 2510 Planarity : 0.004 0.056 1918 Dihedral : 29.176 170.467 4518 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.02 % Allowed : 17.25 % Favored : 80.74 % 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: 2.57 (0.25), residues: 1179 helix: 2.62 (0.18), residues: 826 sheet: -2.01 (1.43), residues: 16 loop : -0.48 (0.34), residues: 337 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 0.022 0.001 TYR H 83 ARG 0.008 0.000 ARG D 86 *********************** 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 185 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 1.315 Fit side-chains revert: symmetry clash REVERT: C 110 ASN cc_start: 0.7969 (t0) cc_final: 0.7726 (p0) outliers start: 18 outliers final: 12 residues processed: 182 average time/residue: 0.2877 time to fit residues: 76.5159 Evaluate side-chains 172 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 1.381 ------------------------------------------------------------------------------- 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 H residue 47 GLN Chi-restraints excluded: chain K residue 254 LEU 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 135 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 86 optimal weight: 30.0000 overall best weight: 4.1186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 15912 Z= 0.417 Angle : 0.636 9.072 22722 Z= 0.363 Chirality : 0.039 0.139 2510 Planarity : 0.004 0.054 1918 Dihedral : 29.440 170.993 4518 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.90 % Allowed : 17.47 % 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: 2.36 (0.25), residues: 1179 helix: 2.44 (0.18), residues: 826 sheet: -1.99 (1.42), residues: 16 loop : -0.50 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 220 HIS 0.008 0.001 HIS B 75 PHE 0.011 0.001 PHE C 25 TYR 0.028 0.002 TYR B 88 ARG 0.008 0.000 ARG D 86 *********************** 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 176 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 1.238 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 14 residues processed: 172 average time/residue: 0.2798 time to fit residues: 70.8555 Evaluate side-chains 170 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 B residue 49 LEU Chi-restraints excluded: chain C residue 64 GLU 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 G residue 16 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain K residue 254 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2423 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= 0.206 Angle : 0.571 9.187 22722 Z= 0.331 Chirality : 0.034 0.142 2510 Planarity : 0.004 0.057 1918 Dihedral : 29.197 169.652 4518 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.12 % Favored : 97.79 % Rotamer: Outliers : 1.79 % Allowed : 17.92 % Favored : 80.29 % 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: 2.59 (0.25), residues: 1179 helix: 2.59 (0.18), residues: 827 sheet: -2.03 (1.40), residues: 16 loop : -0.35 (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 0.020 0.001 PHE K 186 TYR 0.020 0.001 TYR B 88 ARG 0.009 0.000 ARG D 86 *********************** 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 192 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 189 average time/residue: 0.2925 time to fit residues: 79.9133 Evaluate side-chains 174 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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 B residue 49 LEU Chi-restraints excluded: chain C residue 64 GLU 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 K residue 254 LEU 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 122 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 chunk 117 optimal weight: 30.0000 chunk 123 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15912 Z= 0.281 Angle : 0.595 10.418 22722 Z= 0.344 Chirality : 0.035 0.143 2510 Planarity : 0.004 0.075 1918 Dihedral : 29.232 169.519 4518 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.54 % Rotamer: Outliers : 1.57 % Allowed : 19.26 % Favored : 79.17 % 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: 2.51 (0.25), residues: 1179 helix: 2.52 (0.18), residues: 826 sheet: -1.95 (1.41), residues: 16 loop : -0.35 (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 0.010 0.001 PHE A 67 TYR 0.061 0.002 TYR F 88 ARG 0.010 0.000 ARG D 86 *********************** 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 175 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 14 residues processed: 172 average time/residue: 0.2953 time to fit residues: 73.5091 Evaluate side-chains 172 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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 B residue 49 LEU Chi-restraints excluded: chain C residue 64 GLU 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 G residue 16 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain K residue 254 LEU 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 137 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2586 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= 0.237 Angle : 0.596 11.090 22722 Z= 0.343 Chirality : 0.035 0.141 2510 Planarity : 0.004 0.068 1918 Dihedral : 29.169 168.979 4518 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.21 % Favored : 97.71 % Rotamer: Outliers : 1.34 % Allowed : 19.71 % Favored : 78.95 % 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: -1.81 (1.43), residues: 16 loop : -0.35 (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 0.020 0.001 PHE K 186 TYR 0.083 0.003 TYR D 83 ARG 0.009 0.000 ARG D 86 ********************** 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 174 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 172 average time/residue: 0.2917 time to fit residues: 72.9351 Evaluate side-chains 168 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR 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 K residue 254 LEU Chi-restraints excluded: chain K residue 372 ILE Chi-restraints excluded: chain K residue 375 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.097909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.064320 restraints weight = 44827.371| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.49 r_work: 0.2878 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2788 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= 0.202 Angle : 0.593 11.117 22722 Z= 0.342 Chirality : 0.034 0.144 2510 Planarity : 0.005 0.077 1918 Dihedral : 29.080 168.312 4518 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.21 % Favored : 97.71 % Rotamer: Outliers : 1.57 % Allowed : 20.16 % Favored : 78.28 % 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: 2.54 (0.25), residues: 1179 helix: 2.51 (0.18), residues: 827 sheet: -1.70 (1.46), residues: 16 loop : -0.28 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 220 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE A 67 TYR 0.107 0.002 TYR D 83 ARG 0.009 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2642.50 seconds wall clock time: 49 minutes 14.57 seconds (2954.57 seconds total)