Starting phenix.real_space_refine on Tue Sep 24 21:39:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5b_29738/09_2024/8g5b_29738.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5b_29738/09_2024/8g5b_29738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5b_29738/09_2024/8g5b_29738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5b_29738/09_2024/8g5b_29738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5b_29738/09_2024/8g5b_29738.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5b_29738/09_2024/8g5b_29738.cif" } resolution = 3.1 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= 0.006 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 41 5.16 5 C 5682 2.51 5 N 1503 2.21 5 O 1783 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9009 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2100 Classifications: {'peptide': 270} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 252} Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "I" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1639 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain: "J" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1012 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "L" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 861 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 106} Chain: "M" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1647 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Chain: "N" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 775 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 97} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N VAL A 78 " occ=0.43 ... (5 atoms not shown) pdb=" CG2 VAL A 78 " occ=0.43 residue: pdb=" N ARG A 207 " occ=0.48 ... (9 atoms not shown) pdb=" NH2 ARG A 207 " occ=0.48 residue: pdb=" N SER A 227 " occ=0.54 ... (4 atoms not shown) pdb=" OG SER A 227 " occ=0.54 residue: pdb=" N SER A 228 " occ=0.54 ... (4 atoms not shown) pdb=" OG SER A 228 " occ=0.54 residue: pdb=" N TRP A 234 " occ=0.52 ... (12 atoms not shown) pdb=" CH2 TRP A 234 " occ=0.52 residue: pdb=" N MET A 260 " occ=0.50 ... (6 atoms not shown) pdb=" CE MET A 260 " occ=0.50 residue: pdb=" N ILE A 274 " occ=0.62 ... (6 atoms not shown) pdb=" CD1 ILE A 274 " occ=0.62 residue: pdb=" N ASP A 275 " occ=0.62 ... (6 atoms not shown) pdb=" OD2 ASP A 275 " occ=0.62 Time building chain proxies: 5.91, per 1000 atoms: 0.66 Number of scatterers: 9009 At special positions: 0 Unit cell: (94.875, 123.75, 136.95, 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 41 16.00 O 1783 8.00 N 1503 7.00 C 5682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 93 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 200 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 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 Links applied NAG-ASN " NAG A 401 " - " ASN A 165 " " NAG A 402 " - " ASN A 285 " Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 32 sheets defined 9.7% alpha, 46.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.735A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.711A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 84 through 88 Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 160 through 162 No H-bonds generated for 'chain 'I' and resid 160 through 162' Processing helix chain 'I' and resid 191 through 196 removed outlier: 3.983A pdb=" N THR I 195 " --> pdb=" O SER I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 208 Processing helix chain 'J' and resid 88 through 92 Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.877A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.970A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 127 removed outlier: 3.636A pdb=" N SER M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 188 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.680A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 54 removed outlier: 7.081A pdb=" N CYS A 277 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.785A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.722A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA7, first strand: chain 'A' and resid 164 through 169 removed outlier: 5.109A pdb=" N ARG A 201 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.287A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.287A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS H 96 " --> pdb=" O TRP H 110 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TRP H 110 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG H 98 " --> pdb=" O ASP H 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.280A pdb=" N ILE I 34 " --> pdb=" O GLU I 50 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY I 44 " --> pdb=" O ARG I 40 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER I 57 " --> pdb=" O LEU I 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.845A pdb=" N TYR I 106 " --> pdb=" O ARG I 95 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 124 through 128 removed outlier: 6.016A pdb=" N TYR I 180 " --> pdb=" O ASP I 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 124 through 128 removed outlier: 6.016A pdb=" N TYR I 180 " --> pdb=" O ASP I 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 155 through 158 removed outlier: 3.923A pdb=" N TYR I 198 " --> pdb=" O VAL I 215 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.209A pdb=" N TRP J 36 " --> pdb=" O TYR J 52 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR J 52 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TRP J 38 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR J 42 " --> pdb=" O GLY J 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.686A pdb=" N CYS J 97 " --> pdb=" O TRP J 120 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TRP J 120 " --> pdb=" O CYS J 97 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ARG J 99 " --> pdb=" O ASP J 118 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AC4, first strand: chain 'L' and resid 11 through 12 removed outlier: 5.429A pdb=" N ASN L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU L 42 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU L 51 " --> pdb=" O LEU L 42 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 11 through 12 removed outlier: 5.429A pdb=" N ASN L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.841A pdb=" N ASP M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.147A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 10 through 13 removed outlier: 4.004A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 114 through 118 removed outlier: 5.661A pdb=" N TYR M 173 " --> pdb=" O ASN M 138 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 153 through 155 removed outlier: 4.323A pdb=" N TRP M 148 " --> pdb=" O GLN M 155 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.828A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 12 through 13 Processing sheet with id=AD4, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.425A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.425A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 993 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: 3.26 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2842 1.34 - 1.46: 2359 1.46 - 1.59: 3964 1.59 - 1.71: 0 1.71 - 1.84: 58 Bond restraints: 9223 Sorted by residual: bond pdb=" N VAL L 13 " pdb=" CA VAL L 13 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.77e+00 bond pdb=" N ILE A 182 " pdb=" CA ILE A 182 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.29e-02 6.01e+03 7.52e+00 bond pdb=" N ILE M 21 " pdb=" CA ILE M 21 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.45e+00 bond pdb=" N THR L 5 " pdb=" CA THR L 5 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.79e+00 bond pdb=" N GLU J 103 " pdb=" CA GLU J 103 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.27e-02 6.20e+03 6.39e+00 ... (remaining 9218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 12275 1.89 - 3.79: 232 3.79 - 5.68: 23 5.68 - 7.58: 1 7.58 - 9.47: 1 Bond angle restraints: 12532 Sorted by residual: angle pdb=" C GLU M 93 " pdb=" CA GLU M 93 " pdb=" CB GLU M 93 " ideal model delta sigma weight residual 112.99 103.52 9.47 2.10e+00 2.27e-01 2.03e+01 angle pdb=" C ASP M 151 " pdb=" CA ASP M 151 " pdb=" CB ASP M 151 " ideal model delta sigma weight residual 115.79 111.19 4.60 1.19e+00 7.06e-01 1.50e+01 angle pdb=" N PRO M 95 " pdb=" CA PRO M 95 " pdb=" CB PRO M 95 " ideal model delta sigma weight residual 103.25 107.09 -3.84 1.05e+00 9.07e-01 1.34e+01 angle pdb=" CA PRO M 95 " pdb=" N PRO M 95 " pdb=" CD PRO M 95 " ideal model delta sigma weight residual 112.00 107.29 4.71 1.40e+00 5.10e-01 1.13e+01 angle pdb=" CA GLU M 93 " pdb=" C GLU M 93 " pdb=" O GLU M 93 " ideal model delta sigma weight residual 121.98 118.40 3.58 1.13e+00 7.83e-01 1.00e+01 ... (remaining 12527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5063 17.66 - 35.33: 313 35.33 - 52.99: 89 52.99 - 70.65: 16 70.65 - 88.31: 16 Dihedral angle restraints: 5497 sinusoidal: 2139 harmonic: 3358 Sorted by residual: dihedral pdb=" CB CYS A 281 " pdb=" SG CYS A 281 " pdb=" SG CYS A 305 " pdb=" CB CYS A 305 " ideal model delta sinusoidal sigma weight residual 93.00 25.88 67.12 1 1.00e+01 1.00e-02 5.87e+01 dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 97 " pdb=" CB CYS J 97 " ideal model delta sinusoidal sigma weight residual 93.00 46.98 46.02 1 1.00e+01 1.00e-02 2.93e+01 dihedral pdb=" CB CYS M 134 " pdb=" SG CYS M 134 " pdb=" SG CYS M 194 " pdb=" CB CYS M 194 " ideal model delta sinusoidal sigma weight residual 93.00 55.11 37.89 1 1.00e+01 1.00e-02 2.02e+01 ... (remaining 5494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1249 0.081 - 0.162: 135 0.162 - 0.243: 4 0.243 - 0.324: 0 0.324 - 0.405: 2 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA GLU M 93 " pdb=" N GLU M 93 " pdb=" C GLU M 93 " pdb=" CB GLU M 93 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CA TYR M 94 " pdb=" N TYR M 94 " pdb=" C TYR M 94 " pdb=" CB TYR M 94 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA ILE A 182 " pdb=" N ILE A 182 " pdb=" C ILE A 182 " pdb=" CB ILE A 182 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1387 not shown) Planarity restraints: 1599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR M 94 " -0.067 5.00e-02 4.00e+02 9.85e-02 1.55e+01 pdb=" N PRO M 95 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO M 95 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO M 95 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 292 " 0.065 5.00e-02 4.00e+02 9.74e-02 1.52e+01 pdb=" N PRO A 293 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO A 293 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 293 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN L 11 " -0.058 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO L 12 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO L 12 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO L 12 " -0.046 5.00e-02 4.00e+02 ... (remaining 1596 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1074 2.75 - 3.28: 8684 3.28 - 3.82: 14851 3.82 - 4.36: 18597 4.36 - 4.90: 32730 Nonbonded interactions: 75936 Sorted by model distance: nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 114 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR A 98 " pdb=" OG SER A 228 " model vdw 2.236 3.040 nonbonded pdb=" OE2 GLU M 195 " pdb=" OG1 THR M 206 " model vdw 2.243 3.040 nonbonded pdb=" O GLU M 187 " pdb=" NH2 ARG M 211 " model vdw 2.257 3.120 nonbonded pdb=" O PRO J 14 " pdb=" OG SER J 15 " model vdw 2.289 3.040 ... (remaining 75931 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 0.710 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.980 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 : 0.006 0.042 9223 Z= 0.381 Angle : 0.628 9.473 12532 Z= 0.365 Chirality : 0.047 0.405 1390 Planarity : 0.005 0.098 1597 Dihedral : 13.651 88.313 3327 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.70 % Allowed : 0.80 % Favored : 98.50 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 12.28 % 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: 0.40 (0.25), residues: 1157 helix: 0.62 (0.79), residues: 42 sheet: 0.43 (0.23), residues: 506 loop : 0.23 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 47 HIS 0.004 0.001 HIS M 91 PHE 0.017 0.001 PHE N 46 TYR 0.020 0.002 TYR J 35 ARG 0.005 0.001 ARG M 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 193 time to evaluate : 0.831 Fit side-chains REVERT: A 110 SER cc_start: 0.8084 (t) cc_final: 0.7518 (m) REVERT: A 140 LYS cc_start: 0.7826 (mmtm) cc_final: 0.7234 (mmtt) REVERT: H 23 LYS cc_start: 0.7968 (tptp) cc_final: 0.7725 (tptt) REVERT: H 34 MET cc_start: 0.8098 (mmm) cc_final: 0.7830 (tpp) REVERT: H 46 GLU cc_start: 0.8032 (tt0) cc_final: 0.7708 (tt0) REVERT: H 65 LYS cc_start: 0.8094 (ttpt) cc_final: 0.7742 (ttmt) REVERT: I 3 GLN cc_start: 0.8187 (pt0) cc_final: 0.7929 (pt0) REVERT: I 5 GLN cc_start: 0.7847 (tp40) cc_final: 0.7620 (tp40) REVERT: I 23 LYS cc_start: 0.8014 (ttmt) cc_final: 0.7778 (tttm) REVERT: I 65 LYS cc_start: 0.8029 (tppt) cc_final: 0.7635 (tptp) REVERT: I 210 LYS cc_start: 0.7970 (tttp) cc_final: 0.7494 (ttpt) REVERT: I 213 LYS cc_start: 0.6977 (tptt) cc_final: 0.6695 (tptt) REVERT: J 25 SER cc_start: 0.7840 (m) cc_final: 0.7482 (p) REVERT: J 45 LYS cc_start: 0.8383 (mttp) cc_final: 0.7722 (mtpt) REVERT: J 91 ASP cc_start: 0.8500 (m-30) cc_final: 0.8156 (m-30) REVERT: L 27 LYS cc_start: 0.7577 (ttmt) cc_final: 0.6781 (tttm) REVERT: L 75 ASP cc_start: 0.6888 (p0) cc_final: 0.6419 (m-30) REVERT: M 77 SER cc_start: 0.8093 (p) cc_final: 0.7883 (t) REVERT: M 165 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6925 (mm-30) REVERT: M 183 LYS cc_start: 0.7558 (tttm) cc_final: 0.7349 (tttt) REVERT: N 65 SER cc_start: 0.8367 (t) cc_final: 0.8082 (m) REVERT: N 96 GLN cc_start: 0.8220 (mp10) cc_final: 0.7819 (mp10) outliers start: 7 outliers final: 2 residues processed: 198 average time/residue: 0.2327 time to fit residues: 62.6018 Evaluate side-chains 142 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain M residue 93 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 189 GLN H 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9223 Z= 0.324 Angle : 0.640 8.084 12532 Z= 0.337 Chirality : 0.047 0.206 1390 Planarity : 0.005 0.073 1597 Dihedral : 5.778 50.469 1308 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.60 % Allowed : 7.49 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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: 0.42 (0.25), residues: 1157 helix: 0.80 (0.76), residues: 43 sheet: 0.47 (0.22), residues: 515 loop : 0.20 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 36 HIS 0.006 0.001 HIS H 35 PHE 0.016 0.002 PHE N 46 TYR 0.037 0.002 TYR J 35 ARG 0.003 0.001 ARG J 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 146 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 241 ASP cc_start: 0.8146 (t0) cc_final: 0.7727 (t70) REVERT: H 23 LYS cc_start: 0.8109 (tptp) cc_final: 0.7872 (tptt) REVERT: H 31 ARG cc_start: 0.7624 (mtm180) cc_final: 0.7330 (mtt180) REVERT: H 34 MET cc_start: 0.8044 (mmm) cc_final: 0.7748 (tpp) REVERT: H 46 GLU cc_start: 0.7972 (tt0) cc_final: 0.7596 (tt0) REVERT: H 65 LYS cc_start: 0.7973 (ttpt) cc_final: 0.7748 (tttt) REVERT: H 80 TYR cc_start: 0.7804 (m-80) cc_final: 0.7336 (m-80) REVERT: I 65 LYS cc_start: 0.7853 (tppt) cc_final: 0.7399 (tptp) REVERT: I 73 ASP cc_start: 0.7963 (t70) cc_final: 0.7760 (t70) REVERT: J 25 SER cc_start: 0.7961 (m) cc_final: 0.7607 (p) REVERT: J 32 ASN cc_start: 0.8260 (p0) cc_final: 0.8026 (p0) REVERT: J 83 LYS cc_start: 0.7799 (mtpp) cc_final: 0.7593 (mtpt) REVERT: L 27 LYS cc_start: 0.7577 (ttmt) cc_final: 0.6829 (tttm) REVERT: L 65 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.6594 (m-30) REVERT: L 66 ARG cc_start: 0.6877 (mtm-85) cc_final: 0.6578 (mtm110) REVERT: L 87 ASP cc_start: 0.7456 (m-30) cc_final: 0.7206 (m-30) REVERT: M 77 SER cc_start: 0.8193 (p) cc_final: 0.7987 (t) REVERT: M 160 GLN cc_start: 0.6599 (mm-40) cc_final: 0.6323 (mm-40) REVERT: M 165 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6854 (mm-30) REVERT: N 65 SER cc_start: 0.8034 (t) cc_final: 0.7562 (m) REVERT: N 96 GLN cc_start: 0.8280 (mp10) cc_final: 0.8035 (mp10) outliers start: 16 outliers final: 7 residues processed: 154 average time/residue: 0.2040 time to fit residues: 44.4711 Evaluate side-chains 145 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 0.1980 chunk 114 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN I 109 GLN ** I 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN L 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9223 Z= 0.324 Angle : 0.607 7.064 12532 Z= 0.317 Chirality : 0.046 0.184 1390 Planarity : 0.005 0.062 1597 Dihedral : 5.262 49.836 1305 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.90 % Allowed : 9.49 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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: 0.40 (0.24), residues: 1157 helix: 0.86 (0.77), residues: 44 sheet: 0.54 (0.22), residues: 509 loop : 0.09 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 36 HIS 0.005 0.001 HIS H 35 PHE 0.012 0.002 PHE N 46 TYR 0.027 0.002 TYR J 35 ARG 0.003 0.000 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8036 (mt-10) REVERT: A 168 MET cc_start: 0.7795 (mmp) cc_final: 0.7141 (mmt) REVERT: A 241 ASP cc_start: 0.8175 (t0) cc_final: 0.7755 (t0) REVERT: I 65 LYS cc_start: 0.7875 (tppt) cc_final: 0.7391 (tptp) REVERT: J 25 SER cc_start: 0.7983 (m) cc_final: 0.7554 (p) REVERT: L 27 LYS cc_start: 0.7555 (ttmt) cc_final: 0.6815 (tttm) REVERT: L 65 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6433 (m-30) REVERT: L 66 ARG cc_start: 0.6927 (mtm-85) cc_final: 0.6594 (mtm110) REVERT: L 87 ASP cc_start: 0.7410 (m-30) cc_final: 0.7201 (m-30) REVERT: M 160 GLN cc_start: 0.6638 (mm-40) cc_final: 0.6344 (mm-40) REVERT: M 195 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6867 (mm-30) REVERT: N 96 GLN cc_start: 0.8275 (mp10) cc_final: 0.8073 (mp10) outliers start: 29 outliers final: 25 residues processed: 149 average time/residue: 0.2029 time to fit residues: 42.3692 Evaluate side-chains 156 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 100 optimal weight: 0.0270 chunk 30 optimal weight: 8.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN ** I 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN L 55 GLN M 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9223 Z= 0.200 Angle : 0.546 6.893 12532 Z= 0.285 Chirality : 0.043 0.159 1390 Planarity : 0.004 0.056 1597 Dihedral : 4.981 49.955 1303 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.60 % Allowed : 11.39 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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: 0.47 (0.25), residues: 1157 helix: 0.98 (0.76), residues: 45 sheet: 0.54 (0.22), residues: 512 loop : 0.18 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 36 HIS 0.004 0.001 HIS M 91 PHE 0.011 0.001 PHE J 80 TYR 0.019 0.001 TYR J 35 ARG 0.003 0.000 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7910 (mt-10) REVERT: A 168 MET cc_start: 0.7638 (mmp) cc_final: 0.7093 (mmt) REVERT: A 195 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: H 34 MET cc_start: 0.8015 (mmm) cc_final: 0.7719 (tpp) REVERT: H 80 TYR cc_start: 0.7755 (m-80) cc_final: 0.7295 (m-80) REVERT: I 65 LYS cc_start: 0.7793 (tppt) cc_final: 0.7327 (tptp) REVERT: J 25 SER cc_start: 0.7977 (m) cc_final: 0.7532 (p) REVERT: J 45 LYS cc_start: 0.8412 (mttp) cc_final: 0.7779 (mtpt) REVERT: L 27 LYS cc_start: 0.7518 (ttmt) cc_final: 0.6911 (tttm) REVERT: L 65 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6373 (m-30) REVERT: L 66 ARG cc_start: 0.6958 (mtm-85) cc_final: 0.6655 (mtm110) REVERT: M 93 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: M 160 GLN cc_start: 0.6684 (mm-40) cc_final: 0.6399 (mm-40) REVERT: M 195 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7009 (mm-30) REVERT: N 65 SER cc_start: 0.7958 (t) cc_final: 0.7554 (m) REVERT: N 96 GLN cc_start: 0.8159 (mp10) cc_final: 0.7940 (mp10) outliers start: 26 outliers final: 15 residues processed: 153 average time/residue: 0.1987 time to fit residues: 42.4406 Evaluate side-chains 147 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN I 77 ASN L 50 GLN L 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 9223 Z= 0.495 Angle : 0.673 8.612 12532 Z= 0.350 Chirality : 0.048 0.205 1390 Planarity : 0.005 0.058 1597 Dihedral : 5.426 50.446 1303 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.90 % Allowed : 11.69 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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: 0.23 (0.24), residues: 1157 helix: 0.80 (0.76), residues: 44 sheet: 0.42 (0.22), residues: 510 loop : -0.03 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 101 HIS 0.009 0.002 HIS H 35 PHE 0.014 0.002 PHE I 102 TYR 0.028 0.002 TYR J 35 ARG 0.003 0.001 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 135 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 168 MET cc_start: 0.7931 (mmt) cc_final: 0.7322 (mmt) REVERT: H 109 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8329 (m) REVERT: I 5 GLN cc_start: 0.8055 (tp40) cc_final: 0.7766 (tp40) REVERT: I 65 LYS cc_start: 0.7971 (tppt) cc_final: 0.7437 (tptp) REVERT: I 73 ASP cc_start: 0.8123 (t70) cc_final: 0.7818 (t70) REVERT: L 23 CYS cc_start: 0.7782 (t) cc_final: 0.7175 (t) REVERT: L 27 LYS cc_start: 0.7649 (ttmt) cc_final: 0.6941 (tttm) REVERT: L 65 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.6381 (m-30) REVERT: M 24 ARG cc_start: 0.6807 (mtm-85) cc_final: 0.6162 (tmt170) REVERT: M 160 GLN cc_start: 0.6844 (mm-40) cc_final: 0.6562 (mm-40) REVERT: M 195 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7019 (mm-30) REVERT: N 65 SER cc_start: 0.8097 (t) cc_final: 0.7658 (m) REVERT: N 96 GLN cc_start: 0.8274 (mp10) cc_final: 0.8068 (mp10) outliers start: 39 outliers final: 28 residues processed: 162 average time/residue: 0.2141 time to fit residues: 47.8498 Evaluate side-chains 158 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 0.0000 chunk 108 optimal weight: 5.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 GLN L 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9223 Z= 0.182 Angle : 0.544 9.277 12532 Z= 0.283 Chirality : 0.043 0.186 1390 Planarity : 0.004 0.055 1597 Dihedral : 4.973 49.527 1303 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.60 % Allowed : 13.09 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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: 0.35 (0.25), residues: 1157 helix: 1.10 (0.76), residues: 45 sheet: 0.46 (0.22), residues: 520 loop : 0.08 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 36 HIS 0.004 0.001 HIS M 91 PHE 0.013 0.001 PHE J 80 TYR 0.017 0.001 TYR J 35 ARG 0.006 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8029 (mmtm) cc_final: 0.7377 (mmtt) REVERT: H 80 TYR cc_start: 0.7762 (m-80) cc_final: 0.7244 (m-80) REVERT: I 5 GLN cc_start: 0.8048 (tp40) cc_final: 0.7686 (tp40) REVERT: I 65 LYS cc_start: 0.7802 (tppt) cc_final: 0.7332 (tptp) REVERT: I 73 ASP cc_start: 0.8002 (t70) cc_final: 0.7725 (t70) REVERT: J 45 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7753 (mtpt) REVERT: L 27 LYS cc_start: 0.7594 (ttmt) cc_final: 0.6879 (tttm) REVERT: L 65 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6370 (m-30) REVERT: M 160 GLN cc_start: 0.6841 (mm-40) cc_final: 0.6560 (mm-40) REVERT: M 195 GLU cc_start: 0.7506 (mm-30) cc_final: 0.6737 (mm-30) REVERT: N 65 SER cc_start: 0.7957 (t) cc_final: 0.7564 (m) REVERT: N 96 GLN cc_start: 0.8107 (mp10) cc_final: 0.7893 (mp10) outliers start: 26 outliers final: 17 residues processed: 154 average time/residue: 0.2281 time to fit residues: 47.8055 Evaluate side-chains 150 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 59 ASN L 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9223 Z= 0.244 Angle : 0.559 8.330 12532 Z= 0.290 Chirality : 0.044 0.185 1390 Planarity : 0.004 0.054 1597 Dihedral : 4.964 50.085 1303 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.30 % Allowed : 13.09 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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: 0.39 (0.25), residues: 1157 helix: 1.15 (0.77), residues: 45 sheet: 0.50 (0.22), residues: 513 loop : 0.09 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 101 HIS 0.004 0.001 HIS M 91 PHE 0.012 0.001 PHE J 80 TYR 0.019 0.002 TYR J 35 ARG 0.006 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8071 (mmtm) cc_final: 0.7389 (mmtt) REVERT: A 195 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: I 65 LYS cc_start: 0.7826 (tppt) cc_final: 0.7346 (tptp) REVERT: I 73 ASP cc_start: 0.8042 (t70) cc_final: 0.7764 (t70) REVERT: J 45 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7761 (mtpt) REVERT: L 27 LYS cc_start: 0.7590 (ttmt) cc_final: 0.6876 (tttm) REVERT: L 65 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6269 (m-30) REVERT: M 160 GLN cc_start: 0.6849 (mm-40) cc_final: 0.6544 (mm-40) REVERT: M 195 GLU cc_start: 0.7513 (mm-30) cc_final: 0.6755 (mm-30) REVERT: N 65 SER cc_start: 0.7982 (t) cc_final: 0.7621 (m) outliers start: 33 outliers final: 26 residues processed: 161 average time/residue: 0.2241 time to fit residues: 49.5311 Evaluate side-chains 161 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain M residue 85 MET Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 76 optimal weight: 0.0670 chunk 55 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 109 GLN L 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 9223 Z= 0.490 Angle : 0.675 10.943 12532 Z= 0.349 Chirality : 0.048 0.194 1390 Planarity : 0.005 0.056 1597 Dihedral : 5.416 50.302 1303 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.00 % Allowed : 13.09 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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: 0.11 (0.24), residues: 1157 helix: 0.69 (0.75), residues: 45 sheet: 0.36 (0.22), residues: 511 loop : -0.12 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 101 HIS 0.007 0.002 HIS M 91 PHE 0.015 0.002 PHE I 64 TYR 0.027 0.002 TYR J 35 ARG 0.005 0.001 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7462 (mmtt) REVERT: H 46 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: I 23 LYS cc_start: 0.8081 (ttmt) cc_final: 0.7780 (tttm) REVERT: I 63 LYS cc_start: 0.8432 (ttmm) cc_final: 0.8034 (ttmt) REVERT: I 65 LYS cc_start: 0.7976 (tppt) cc_final: 0.7397 (tptp) REVERT: I 73 ASP cc_start: 0.8174 (t70) cc_final: 0.7859 (t70) REVERT: I 109 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: L 23 CYS cc_start: 0.7767 (t) cc_final: 0.7158 (t) REVERT: L 27 LYS cc_start: 0.7639 (ttmt) cc_final: 0.6874 (tttm) REVERT: L 65 ASP cc_start: 0.7037 (OUTLIER) cc_final: 0.6313 (m-30) REVERT: M 24 ARG cc_start: 0.6832 (mtm-85) cc_final: 0.6450 (ttp80) REVERT: M 160 GLN cc_start: 0.6869 (mm-40) cc_final: 0.6583 (mm-40) REVERT: M 183 LYS cc_start: 0.7437 (tttt) cc_final: 0.7224 (tttt) REVERT: M 195 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6749 (mm-30) REVERT: N 65 SER cc_start: 0.8091 (t) cc_final: 0.7657 (m) outliers start: 40 outliers final: 31 residues processed: 158 average time/residue: 0.2556 time to fit residues: 54.6767 Evaluate side-chains 163 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 109 GLN L 50 GLN L 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9223 Z= 0.243 Angle : 0.572 10.519 12532 Z= 0.296 Chirality : 0.044 0.216 1390 Planarity : 0.004 0.054 1597 Dihedral : 5.106 49.468 1303 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.30 % Allowed : 13.99 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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: 0.28 (0.25), residues: 1157 helix: 1.03 (0.76), residues: 45 sheet: 0.45 (0.22), residues: 510 loop : -0.01 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 36 HIS 0.004 0.001 HIS M 91 PHE 0.011 0.001 PHE J 80 TYR 0.017 0.002 TYR J 35 ARG 0.009 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7435 (mmtt) REVERT: H 46 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: I 23 LYS cc_start: 0.8066 (ttmt) cc_final: 0.7787 (tttm) REVERT: I 63 LYS cc_start: 0.8341 (ttmm) cc_final: 0.7943 (ttmt) REVERT: I 65 LYS cc_start: 0.7827 (tppt) cc_final: 0.7354 (tptp) REVERT: I 73 ASP cc_start: 0.8086 (t70) cc_final: 0.7785 (t70) REVERT: L 27 LYS cc_start: 0.7603 (ttmt) cc_final: 0.6825 (tttm) REVERT: L 65 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6347 (m-30) REVERT: M 160 GLN cc_start: 0.6859 (mm-40) cc_final: 0.6556 (mm-40) REVERT: M 195 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6724 (mm-30) REVERT: N 65 SER cc_start: 0.7960 (t) cc_final: 0.7589 (m) outliers start: 33 outliers final: 29 residues processed: 158 average time/residue: 0.2592 time to fit residues: 54.4672 Evaluate side-chains 165 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 9 optimal weight: 0.0870 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 28 optimal weight: 0.0020 overall best weight: 0.8172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9223 Z= 0.159 Angle : 0.528 9.895 12532 Z= 0.274 Chirality : 0.042 0.225 1390 Planarity : 0.004 0.053 1597 Dihedral : 4.787 49.730 1303 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.80 % Allowed : 14.69 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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: 0.43 (0.25), residues: 1157 helix: 1.40 (0.77), residues: 45 sheet: 0.53 (0.23), residues: 516 loop : 0.09 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 36 HIS 0.003 0.001 HIS M 91 PHE 0.011 0.001 PHE J 80 TYR 0.013 0.001 TYR J 35 ARG 0.010 0.001 ARG A 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8037 (mmtm) cc_final: 0.7363 (mmtt) REVERT: H 38 LYS cc_start: 0.8288 (tttt) cc_final: 0.7772 (tttp) REVERT: H 46 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7413 (tt0) REVERT: I 3 GLN cc_start: 0.8010 (pt0) cc_final: 0.7757 (pt0) REVERT: I 23 LYS cc_start: 0.8018 (ttmt) cc_final: 0.7744 (tttm) REVERT: I 63 LYS cc_start: 0.8288 (ttmm) cc_final: 0.7925 (ttmt) REVERT: I 73 ASP cc_start: 0.7974 (t70) cc_final: 0.7711 (t70) REVERT: I 109 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7925 (pt0) REVERT: J 45 LYS cc_start: 0.8331 (mttp) cc_final: 0.7718 (mtpt) REVERT: L 27 LYS cc_start: 0.7551 (ttmt) cc_final: 0.6824 (tttm) REVERT: L 65 ASP cc_start: 0.7013 (OUTLIER) cc_final: 0.6318 (m-30) REVERT: M 160 GLN cc_start: 0.6834 (mm-40) cc_final: 0.6559 (mm-40) REVERT: M 183 LYS cc_start: 0.7237 (tttt) cc_final: 0.7028 (tttt) REVERT: M 195 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6679 (mm-30) REVERT: N 65 SER cc_start: 0.7929 (t) cc_final: 0.7565 (m) outliers start: 28 outliers final: 20 residues processed: 167 average time/residue: 0.2253 time to fit residues: 51.1229 Evaluate side-chains 160 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 94 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN L 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.145526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.107223 restraints weight = 10501.672| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.31 r_work: 0.2726 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2551 r_free = 0.2551 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9223 Z= 0.219 Angle : 0.552 9.829 12532 Z= 0.286 Chirality : 0.043 0.220 1390 Planarity : 0.004 0.055 1597 Dihedral : 4.857 50.240 1303 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.80 % Allowed : 15.38 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.28 % 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: 0.44 (0.25), residues: 1157 helix: 1.26 (0.76), residues: 45 sheet: 0.59 (0.23), residues: 512 loop : 0.05 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 101 HIS 0.004 0.001 HIS M 91 PHE 0.012 0.001 PHE J 80 TYR 0.017 0.001 TYR J 35 ARG 0.009 0.000 ARG A 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2294.98 seconds wall clock time: 42 minutes 6.68 seconds (2526.68 seconds total)