Starting phenix.real_space_refine on Sun Mar 10 17:40:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9r_29874/03_2024/8g9r_29874.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9r_29874/03_2024/8g9r_29874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9r_29874/03_2024/8g9r_29874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9r_29874/03_2024/8g9r_29874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9r_29874/03_2024/8g9r_29874.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g9r_29874/03_2024/8g9r_29874.pdb" } resolution = 3.28 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= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 2315 2.51 5 N 585 2.21 5 O 665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3570 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "B" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "C" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "D" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "E" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Time building chain proxies: 2.46, per 1000 atoms: 0.69 Number of scatterers: 3570 At special positions: 0 Unit cell: (76.54, 92.02, 43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 665 8.00 N 585 7.00 C 2315 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 598.0 milliseconds 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 870 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 51.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 12 through 16 removed outlier: 6.631A pdb=" N LEU B 12 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N LYS D 15 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 14 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 12 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LYS B 15 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 14 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 14 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL E 14 " --> pdb=" O MET C 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 19 through 21 removed outlier: 6.635A pdb=" N VAL B 20 " --> pdb=" O ARG D 21 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL A 20 " --> pdb=" O ARG B 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 30 through 34 removed outlier: 6.806A pdb=" N HIS A 31 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ARG C 34 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE A 33 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N HIS C 31 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ARG E 34 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE C 33 " --> pdb=" O ARG E 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 60 through 80 removed outlier: 9.281A pdb=" N THR B 60 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 10.933A pdb=" N GLU D 63 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU B 62 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N VAL D 65 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE B 64 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N GLY D 67 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N GLU B 66 " --> pdb=" O GLY D 67 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N TYR D 69 " --> pdb=" O GLU B 66 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE B 68 " --> pdb=" O TYR D 69 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N VAL D 71 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS B 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ILE D 73 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N GLU B 72 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR D 75 " --> pdb=" O GLU B 72 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N ASP B 74 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 10.844A pdb=" N SER D 77 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 9.399A pdb=" N LYS B 76 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N TRP D 79 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR B 78 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N THR A 60 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 10.928A pdb=" N GLU B 63 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU A 62 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N VAL B 65 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE A 64 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N GLY B 67 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N GLU A 66 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N TYR B 69 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ILE A 68 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N VAL B 71 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ILE B 73 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N GLU A 72 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR B 75 " --> pdb=" O GLU A 72 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N ASP A 74 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 10.840A pdb=" N SER B 77 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N LYS A 76 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N TRP B 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N TYR A 78 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLU A 61 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLU C 62 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU A 63 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE C 64 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ILE C 68 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N TYR A 69 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ASP C 74 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR A 75 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LYS C 76 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N SER A 77 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR C 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 80 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU C 61 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU E 62 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLU C 63 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE E 64 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE E 68 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR C 69 " --> pdb=" O ILE E 68 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASP E 74 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR C 75 " --> pdb=" O ASP E 74 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LYS E 76 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER C 77 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR E 78 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS E 80 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 92 through 97 removed outlier: 6.839A pdb=" N GLU B 92 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N PHE D 95 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL B 94 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ALA D 97 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR B 96 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLU A 92 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N PHE B 95 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 94 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ALA B 97 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR A 96 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL C 94 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 97 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 94 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA C 97 " --> pdb=" O THR E 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 103 through 110 removed outlier: 6.715A pdb=" N ARG B 104 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ILE D 107 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR B 106 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ALA D 109 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ALA B 108 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG A 104 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ILE B 107 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR A 106 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA B 109 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ALA A 108 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ALA A 109 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU C 110 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ALA C 109 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU E 110 " --> pdb=" O ALA C 109 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 114 through 115 removed outlier: 7.186A pdb=" N TYR B 114 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR A 114 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 115 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 115 " --> pdb=" O TYR E 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 122 removed outlier: 7.021A pdb=" N THR B 119 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL D 122 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL B 121 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR A 119 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N VAL B 122 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 121 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 120 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 120 " --> pdb=" O THR E 119 " (cutoff:3.500A) 56 hydrogen bonds defined for protein. 168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.73 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1110 1.34 - 1.46: 594 1.46 - 1.57: 1941 1.57 - 1.69: 0 1.69 - 1.80: 10 Bond restraints: 3655 Sorted by residual: bond pdb=" CA ASN C 27 " pdb=" C ASN C 27 " ideal model delta sigma weight residual 1.520 1.525 -0.006 1.16e-02 7.43e+03 2.32e-01 bond pdb=" CA ASN A 27 " pdb=" C ASN A 27 " ideal model delta sigma weight residual 1.520 1.525 -0.005 1.16e-02 7.43e+03 2.15e-01 bond pdb=" N ILE C 73 " pdb=" CA ILE C 73 " ideal model delta sigma weight residual 1.457 1.463 -0.006 1.28e-02 6.10e+03 1.99e-01 bond pdb=" N LEU C 17 " pdb=" CA LEU C 17 " ideal model delta sigma weight residual 1.462 1.467 -0.006 1.31e-02 5.83e+03 1.94e-01 bond pdb=" CA ASN B 27 " pdb=" C ASN B 27 " ideal model delta sigma weight residual 1.520 1.525 -0.005 1.16e-02 7.43e+03 1.93e-01 ... (remaining 3650 not shown) Histogram of bond angle deviations from ideal: 101.16 - 107.73: 170 107.73 - 114.30: 2129 114.30 - 120.87: 1434 120.87 - 127.44: 1212 127.44 - 134.01: 30 Bond angle restraints: 4975 Sorted by residual: angle pdb=" N GLY C 67 " pdb=" CA GLY C 67 " pdb=" C GLY C 67 " ideal model delta sigma weight residual 113.18 117.37 -4.19 2.37e+00 1.78e-01 3.13e+00 angle pdb=" N GLY B 67 " pdb=" CA GLY B 67 " pdb=" C GLY B 67 " ideal model delta sigma weight residual 113.18 117.37 -4.19 2.37e+00 1.78e-01 3.12e+00 angle pdb=" N GLY D 67 " pdb=" CA GLY D 67 " pdb=" C GLY D 67 " ideal model delta sigma weight residual 113.18 117.35 -4.17 2.37e+00 1.78e-01 3.10e+00 angle pdb=" N GLY E 67 " pdb=" CA GLY E 67 " pdb=" C GLY E 67 " ideal model delta sigma weight residual 113.18 117.33 -4.15 2.37e+00 1.78e-01 3.07e+00 angle pdb=" N GLY A 67 " pdb=" CA GLY A 67 " pdb=" C GLY A 67 " ideal model delta sigma weight residual 113.18 117.33 -4.15 2.37e+00 1.78e-01 3.07e+00 ... (remaining 4970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 1880 16.91 - 33.82: 195 33.82 - 50.73: 70 50.73 - 67.64: 5 67.64 - 84.55: 10 Dihedral angle restraints: 2160 sinusoidal: 820 harmonic: 1340 Sorted by residual: dihedral pdb=" CG ARG E 21 " pdb=" CD ARG E 21 " pdb=" NE ARG E 21 " pdb=" CZ ARG E 21 " ideal model delta sinusoidal sigma weight residual 180.00 137.63 42.37 2 1.50e+01 4.44e-03 9.69e+00 dihedral pdb=" CG ARG D 21 " pdb=" CD ARG D 21 " pdb=" NE ARG D 21 " pdb=" CZ ARG D 21 " ideal model delta sinusoidal sigma weight residual 180.00 137.65 42.35 2 1.50e+01 4.44e-03 9.68e+00 dihedral pdb=" CG ARG A 21 " pdb=" CD ARG A 21 " pdb=" NE ARG A 21 " pdb=" CZ ARG A 21 " ideal model delta sinusoidal sigma weight residual 180.00 137.66 42.34 2 1.50e+01 4.44e-03 9.68e+00 ... (remaining 2157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 294 0.025 - 0.050: 171 0.050 - 0.075: 45 0.075 - 0.100: 21 0.100 - 0.125: 59 Chirality restraints: 590 Sorted by residual: chirality pdb=" CA VAL C 14 " pdb=" N VAL C 14 " pdb=" C VAL C 14 " pdb=" CB VAL C 14 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA VAL D 121 " pdb=" N VAL D 121 " pdb=" C VAL D 121 " pdb=" CB VAL D 121 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA ILE E 68 " pdb=" N ILE E 68 " pdb=" C ILE E 68 " pdb=" CB ILE E 68 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 587 not shown) Planarity restraints: 610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 101 " -0.045 5.00e-02 4.00e+02 6.88e-02 7.57e+00 pdb=" N PRO D 102 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO D 102 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 102 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 101 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.52e+00 pdb=" N PRO A 102 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 101 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO E 102 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 102 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 102 " -0.038 5.00e-02 4.00e+02 ... (remaining 607 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1743 3.01 - 3.49: 2937 3.49 - 3.96: 4492 3.96 - 4.43: 4746 4.43 - 4.90: 9525 Nonbonded interactions: 23443 Sorted by model distance: nonbonded pdb=" O ASP A 99 " pdb=" O SER C 100 " model vdw 2.542 3.040 nonbonded pdb=" N ASP E 18 " pdb=" OD1 ASP E 18 " model vdw 2.556 2.520 nonbonded pdb=" N ASP A 18 " pdb=" OD1 ASP A 18 " model vdw 2.557 2.520 nonbonded pdb=" N ASP D 18 " pdb=" OD1 ASP D 18 " model vdw 2.557 2.520 nonbonded pdb=" N ASP B 18 " pdb=" OD1 ASP B 18 " model vdw 2.557 2.520 ... (remaining 23438 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.610 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.230 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0613 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 : 0.003 0.014 3655 Z= 0.171 Angle : 0.594 4.442 4975 Z= 0.339 Chirality : 0.049 0.125 590 Planarity : 0.008 0.069 610 Dihedral : 16.845 84.550 1290 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 23.08 % Favored : 76.92 % 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: -3.38 (0.30), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.23), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 79 HIS 0.002 0.001 HIS D 88 PHE 0.008 0.001 PHE D 95 TYR 0.009 0.001 TYR E 114 ARG 0.001 0.000 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: D 79 TRP cc_start: 0.4176 (m-10) cc_final: 0.2471 (m100) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.2691 time to fit residues: 9.7057 Evaluate side-chains 18 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 0.0570 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS C 90 HIS E 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2205 moved from start: 0.7219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3655 Z= 0.325 Angle : 0.824 6.392 4975 Z= 0.451 Chirality : 0.054 0.151 590 Planarity : 0.007 0.057 610 Dihedral : 7.048 20.353 490 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.87 % Allowed : 16.67 % Favored : 78.46 % 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: -3.17 (0.31), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP E 79 HIS 0.012 0.003 HIS E 90 PHE 0.023 0.004 PHE D 33 TYR 0.044 0.003 TYR A 105 ARG 0.006 0.001 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 25 time to evaluate : 0.374 Fit side-chains REVERT: A 13 MET cc_start: 0.2745 (mmt) cc_final: 0.1269 (ptp) REVERT: A 35 LYS cc_start: -0.0266 (ttmt) cc_final: -0.1234 (mttt) REVERT: B 35 LYS cc_start: 0.0317 (ttmt) cc_final: -0.0318 (mttp) REVERT: C 26 ILE cc_start: -0.0534 (OUTLIER) cc_final: -0.1069 (mt) REVERT: C 35 LYS cc_start: -0.0903 (ttmt) cc_final: -0.1152 (mmtt) REVERT: E 26 ILE cc_start: -0.1100 (OUTLIER) cc_final: -0.2092 (pt) outliers start: 19 outliers final: 6 residues processed: 44 average time/residue: 0.3691 time to fit residues: 18.3052 Evaluate side-chains 29 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 21 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 96 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 30.0000 chunk 13 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2952 moved from start: 1.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3655 Z= 0.381 Angle : 0.882 8.322 4975 Z= 0.485 Chirality : 0.055 0.202 590 Planarity : 0.008 0.051 610 Dihedral : 7.650 28.742 490 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 2.82 % Allowed : 19.74 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.80 (0.28), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.22), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP E 79 HIS 0.006 0.002 HIS E 90 PHE 0.029 0.004 PHE E 33 TYR 0.021 0.003 TYR B 105 ARG 0.006 0.001 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 31 time to evaluate : 0.363 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 40 average time/residue: 0.1405 time to fit residues: 7.4516 Evaluate side-chains 34 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3336 moved from start: 1.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3655 Z= 0.371 Angle : 0.903 8.567 4975 Z= 0.498 Chirality : 0.056 0.205 590 Planarity : 0.007 0.053 610 Dihedral : 8.128 33.988 490 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 4.10 % Allowed : 21.28 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.98 (0.30), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.23), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP E 79 HIS 0.007 0.002 HIS A 90 PHE 0.022 0.004 PHE A 87 TYR 0.029 0.004 TYR A 105 ARG 0.004 0.001 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 36 time to evaluate : 0.391 Fit side-chains REVERT: E 104 ARG cc_start: 0.5038 (OUTLIER) cc_final: 0.2901 (mtt180) outliers start: 16 outliers final: 10 residues processed: 48 average time/residue: 0.2064 time to fit residues: 11.9933 Evaluate side-chains 44 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 104 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.0030 chunk 17 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 30 optimal weight: 0.0060 chunk 0 optimal weight: 40.0000 chunk 22 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.9810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3184 moved from start: 1.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3655 Z= 0.199 Angle : 0.643 7.805 4975 Z= 0.349 Chirality : 0.050 0.159 590 Planarity : 0.005 0.053 610 Dihedral : 6.556 24.215 490 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 3.08 % Allowed : 24.10 % Favored : 72.82 % 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: -3.72 (0.31), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 79 HIS 0.002 0.001 HIS C 88 PHE 0.019 0.003 PHE D 87 TYR 0.013 0.002 TYR A 114 ARG 0.004 0.000 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 35 time to evaluate : 0.476 Fit side-chains REVERT: E 13 MET cc_start: 0.4186 (ptp) cc_final: 0.3285 (ppp) outliers start: 12 outliers final: 11 residues processed: 42 average time/residue: 0.2021 time to fit residues: 10.1947 Evaluate side-chains 41 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 30 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 40.0000 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3327 moved from start: 1.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3655 Z= 0.229 Angle : 0.688 7.224 4975 Z= 0.370 Chirality : 0.050 0.167 590 Planarity : 0.005 0.046 610 Dihedral : 6.580 24.059 490 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 4.10 % Allowed : 23.59 % Favored : 72.31 % 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: -3.69 (0.31), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP E 79 HIS 0.003 0.001 HIS B 90 PHE 0.021 0.003 PHE E 95 TYR 0.021 0.002 TYR D 105 ARG 0.003 0.000 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 34 time to evaluate : 0.329 Fit side-chains REVERT: A 112 SER cc_start: 0.5128 (OUTLIER) cc_final: 0.4809 (m) REVERT: D 88 HIS cc_start: 0.2806 (OUTLIER) cc_final: 0.2557 (p-80) REVERT: E 13 MET cc_start: 0.4290 (ptp) cc_final: 0.3456 (ppp) outliers start: 16 outliers final: 9 residues processed: 46 average time/residue: 0.1303 time to fit residues: 7.7183 Evaluate side-chains 43 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3260 moved from start: 1.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3655 Z= 0.175 Angle : 0.630 10.349 4975 Z= 0.327 Chirality : 0.049 0.151 590 Planarity : 0.005 0.057 610 Dihedral : 5.944 21.170 490 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.33 % Allowed : 24.36 % Favored : 72.31 % 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: -3.57 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 79 HIS 0.001 0.000 HIS B 90 PHE 0.020 0.002 PHE C 95 TYR 0.011 0.002 TYR A 114 ARG 0.002 0.000 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 34 time to evaluate : 0.402 Fit side-chains REVERT: E 104 ARG cc_start: 0.5077 (OUTLIER) cc_final: 0.3253 (mtt180) outliers start: 13 outliers final: 11 residues processed: 42 average time/residue: 0.1766 time to fit residues: 9.2399 Evaluate side-chains 44 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 32 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 0.0270 chunk 12 optimal weight: 8.9990 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3262 moved from start: 1.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3655 Z= 0.162 Angle : 0.630 14.340 4975 Z= 0.318 Chirality : 0.048 0.148 590 Planarity : 0.005 0.062 610 Dihedral : 5.677 20.995 490 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 3.59 % Allowed : 24.62 % Favored : 71.79 % 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: -3.44 (0.33), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 79 HIS 0.002 0.000 HIS B 90 PHE 0.019 0.002 PHE C 95 TYR 0.012 0.002 TYR A 105 ARG 0.002 0.000 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 31 time to evaluate : 0.403 Fit side-chains REVERT: E 104 ARG cc_start: 0.5027 (OUTLIER) cc_final: 0.3261 (mtt90) outliers start: 14 outliers final: 12 residues processed: 40 average time/residue: 0.2071 time to fit residues: 10.0619 Evaluate side-chains 43 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 30 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3378 moved from start: 1.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3655 Z= 0.192 Angle : 0.657 12.278 4975 Z= 0.338 Chirality : 0.048 0.152 590 Planarity : 0.005 0.058 610 Dihedral : 5.941 21.602 490 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.85 % Allowed : 24.10 % Favored : 72.05 % 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: -3.48 (0.33), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 79 HIS 0.003 0.001 HIS B 90 PHE 0.020 0.002 PHE E 95 TYR 0.013 0.002 TYR C 105 ARG 0.010 0.001 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 35 time to evaluate : 0.419 Fit side-chains REVERT: E 89 GLU cc_start: 0.5585 (tm-30) cc_final: 0.4231 (tp30) REVERT: E 104 ARG cc_start: 0.5102 (OUTLIER) cc_final: 0.3253 (mtt90) outliers start: 15 outliers final: 11 residues processed: 46 average time/residue: 0.1838 time to fit residues: 10.3856 Evaluate side-chains 46 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 34 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3344 moved from start: 1.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3655 Z= 0.171 Angle : 0.624 12.682 4975 Z= 0.319 Chirality : 0.048 0.145 590 Planarity : 0.005 0.064 610 Dihedral : 5.693 21.446 490 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.33 % Allowed : 24.36 % Favored : 72.31 % 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: -3.43 (0.34), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 79 HIS 0.002 0.001 HIS B 90 PHE 0.019 0.002 PHE C 95 TYR 0.012 0.002 TYR C 78 ARG 0.007 0.001 ARG C 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 31 time to evaluate : 0.394 Fit side-chains REVERT: E 104 ARG cc_start: 0.5091 (OUTLIER) cc_final: 0.3372 (mtt180) outliers start: 13 outliers final: 11 residues processed: 39 average time/residue: 0.1778 time to fit residues: 8.6219 Evaluate side-chains 43 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 31 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 1 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5287 r_free = 0.5287 target = 0.238489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.203180 restraints weight = 5565.719| |-----------------------------------------------------------------------------| r_work (start): 0.4968 rms_B_bonded: 5.31 r_work (final): 0.4968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3231 moved from start: 1.6290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3655 Z= 0.221 Angle : 0.691 12.413 4975 Z= 0.362 Chirality : 0.049 0.158 590 Planarity : 0.006 0.064 610 Dihedral : 6.368 25.606 490 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 3.08 % Allowed : 24.10 % Favored : 72.82 % 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: -3.56 (0.33), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 79 HIS 0.004 0.001 HIS E 90 PHE 0.021 0.002 PHE E 95 TYR 0.013 0.002 TYR C 105 ARG 0.007 0.001 ARG C 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1149.12 seconds wall clock time: 21 minutes 28.15 seconds (1288.15 seconds total)