Starting phenix.real_space_refine on Sun Mar 10 20:30:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez8_28730/03_2024/8ez8_28730.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez8_28730/03_2024/8ez8_28730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez8_28730/03_2024/8ez8_28730.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez8_28730/03_2024/8ez8_28730.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez8_28730/03_2024/8ez8_28730.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez8_28730/03_2024/8ez8_28730.pdb" } resolution = 2.78 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= 0.002 sd= 0.068 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 28 5.16 5 C 2997 2.51 5 N 838 2.21 5 O 984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "L ASP 85": "OD1" <-> "OD2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 309": "OD1" <-> "OD2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A ASP 460": "OD1" <-> "OD2" 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: 4847 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 951 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "L" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 786 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2996 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 371} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.46, per 1000 atoms: 0.71 Number of scatterers: 4847 At special positions: 0 Unit cell: (76.32, 96.46, 92.22, 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 28 16.00 O 984 8.00 N 838 7.00 C 2997 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.04 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 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 Links applied ALPHA1-2 " MAN B 4 " - " MAN B 5 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 502 " - " ASN A 146 " " NAG A 503 " - " ASN A 234 " " NAG A 504 " - " ASN A 329 " " NAG B 1 " - " ASN A 200 " Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 924.5 milliseconds 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1106 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 11 sheets defined 4.2% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.007A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.637A pdb=" N GLU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.664A pdb=" N ALA A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.573A pdb=" N SER A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN A 146 " --> pdb=" O GLY A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.252A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.884A pdb=" N SER L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.884A pdb=" N SER L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 16 through 24 removed outlier: 4.127A pdb=" N GLN L 17 " --> pdb=" O GLY L 77 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY L 77 " --> pdb=" O GLN L 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.587A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 125 removed outlier: 4.647A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLN A 173 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.566A pdb=" N SER A 179 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 231 through 233 removed outlier: 3.751A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR A 252 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE A 254 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE A 256 " --> pdb=" O VAL A 263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 279 through 283 Processing sheet with id=AB2, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.703A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N SER A 372 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASP A 399 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS A 378 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) 156 hydrogen bonds defined for protein. 414 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: 1.48 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1593 1.35 - 1.47: 1277 1.47 - 1.59: 2051 1.59 - 1.71: 0 1.71 - 1.83: 34 Bond restraints: 4955 Sorted by residual: bond pdb=" C1 MAN B 4 " pdb=" C2 MAN B 4 " ideal model delta sigma weight residual 1.526 1.558 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C5 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.418 1.448 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C5 MAN B 5 " pdb=" O5 MAN B 5 " ideal model delta sigma weight residual 1.418 1.446 -0.028 2.00e-02 2.50e+03 2.01e+00 ... (remaining 4950 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.98: 167 106.98 - 113.73: 2776 113.73 - 120.48: 1672 120.48 - 127.22: 2039 127.22 - 133.97: 75 Bond angle restraints: 6729 Sorted by residual: angle pdb=" C ARG A 430 " pdb=" N LYS A 431 " pdb=" CA LYS A 431 " ideal model delta sigma weight residual 121.70 126.88 -5.18 1.80e+00 3.09e-01 8.29e+00 angle pdb=" CA CYS A 230 " pdb=" CB CYS A 230 " pdb=" SG CYS A 230 " ideal model delta sigma weight residual 114.40 120.11 -5.71 2.30e+00 1.89e-01 6.16e+00 angle pdb=" C HIS A 336 " pdb=" N CYS A 337 " pdb=" CA CYS A 337 " ideal model delta sigma weight residual 122.07 125.45 -3.38 1.43e+00 4.89e-01 5.59e+00 angle pdb=" C SER L 50 " pdb=" N ASN L 51 " pdb=" CA ASN L 51 " ideal model delta sigma weight residual 121.54 125.70 -4.16 1.91e+00 2.74e-01 4.75e+00 angle pdb=" C3 MAN B 4 " pdb=" C2 MAN B 4 " pdb=" O2 MAN B 4 " ideal model delta sigma weight residual 111.77 105.25 6.52 3.00e+00 1.11e-01 4.72e+00 ... (remaining 6724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.55: 2711 21.55 - 43.09: 279 43.09 - 64.64: 43 64.64 - 86.19: 13 86.19 - 107.73: 6 Dihedral angle restraints: 3052 sinusoidal: 1307 harmonic: 1745 Sorted by residual: dihedral pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " pdb=" SG CYS A 417 " pdb=" CB CYS A 417 " ideal model delta sinusoidal sigma weight residual 93.00 37.74 55.26 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CA ALA A 177 " pdb=" C ALA A 177 " pdb=" N TRP A 178 " pdb=" CA TRP A 178 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 58.52 34.48 1 1.00e+01 1.00e-02 1.69e+01 ... (remaining 3049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 592 0.053 - 0.105: 123 0.105 - 0.158: 35 0.158 - 0.210: 2 0.210 - 0.263: 1 Chirality restraints: 753 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C1 NAG A 504 " pdb=" ND2 ASN A 329 " pdb=" C2 NAG A 504 " pdb=" O5 NAG A 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" C2 MAN B 4 " pdb=" C1 MAN B 4 " pdb=" C3 MAN B 4 " pdb=" O2 MAN B 4 " both_signs ideal model delta sigma weight residual False 2.52 2.67 -0.16 2.00e-01 2.50e+01 6.31e-01 ... (remaining 750 not shown) Planarity restraints: 866 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 7 " 0.032 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO L 8 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 78 " -0.010 2.00e-02 2.50e+03 7.48e-03 9.80e-01 pdb=" CG PHE H 78 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE H 78 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE H 78 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE H 78 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE H 78 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE H 78 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 39 " 0.005 2.00e-02 2.50e+03 9.72e-03 9.44e-01 pdb=" C GLN H 39 " -0.017 2.00e-02 2.50e+03 pdb=" O GLN H 39 " 0.006 2.00e-02 2.50e+03 pdb=" N PRO H 40 " 0.006 2.00e-02 2.50e+03 ... (remaining 863 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 50 2.53 - 3.13: 3649 3.13 - 3.72: 7634 3.72 - 4.31: 11502 4.31 - 4.90: 19416 Nonbonded interactions: 42251 Sorted by model distance: nonbonded pdb=" NE ARG A 403 " pdb=" OE1 GLN A 432 " model vdw 1.943 2.520 nonbonded pdb=" CZ ARG A 403 " pdb=" OE1 GLN A 432 " model vdw 2.202 3.270 nonbonded pdb=" O VAL A 317 " pdb=" OG SER A 335 " model vdw 2.245 2.440 nonbonded pdb=" OG SER A 279 " pdb=" O GLY A 351 " model vdw 2.249 2.440 nonbonded pdb=" OH TYR A 121 " pdb=" OG SER A 182 " model vdw 2.258 2.440 ... (remaining 42246 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.020 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: 9.770 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.980 Find NCS groups from input model: 0.130 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:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.004 0.033 4955 Z= 0.243 Angle : 0.621 6.728 6729 Z= 0.317 Chirality : 0.048 0.263 753 Planarity : 0.003 0.050 862 Dihedral : 17.323 107.734 1913 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.07 % Favored : 95.77 % Rotamer: Outliers : 1.89 % Allowed : 26.65 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.51 (0.35), residues: 615 helix: -1.81 (1.45), residues: 12 sheet: 0.00 (0.34), residues: 226 loop : -0.45 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 34 HIS 0.004 0.001 HIS A 347 PHE 0.017 0.002 PHE H 78 TYR 0.013 0.001 TYR A 121 ARG 0.003 0.000 ARG H 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.597 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 80 average time/residue: 0.8690 time to fit residues: 73.4785 Evaluate side-chains 79 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.0870 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 0.0030 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.5572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.0418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4955 Z= 0.162 Angle : 0.505 7.071 6729 Z= 0.266 Chirality : 0.046 0.153 753 Planarity : 0.003 0.045 862 Dihedral : 9.141 66.990 863 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.74 % Favored : 96.10 % Rotamer: Outliers : 3.59 % Allowed : 26.09 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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 (0.35), residues: 615 helix: -1.81 (1.42), residues: 12 sheet: -0.03 (0.34), residues: 227 loop : -0.33 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 34 HIS 0.002 0.001 HIS A 336 PHE 0.016 0.002 PHE H 78 TYR 0.011 0.001 TYR A 121 ARG 0.004 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 0.540 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 84 average time/residue: 0.8600 time to fit residues: 76.4032 Evaluate side-chains 79 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 390 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 50.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4955 Z= 0.305 Angle : 0.553 8.552 6729 Z= 0.289 Chirality : 0.047 0.162 753 Planarity : 0.003 0.041 862 Dihedral : 8.262 56.084 854 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.55 % Favored : 95.28 % Rotamer: Outliers : 4.91 % Allowed : 24.95 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.55 (0.35), residues: 615 helix: -1.97 (1.39), residues: 12 sheet: -0.16 (0.33), residues: 238 loop : -0.37 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.003 0.001 HIS A 336 PHE 0.021 0.002 PHE H 78 TYR 0.014 0.001 TYR A 121 ARG 0.002 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 74 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: H 100 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8124 (mtm180) REVERT: A 162 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7867 (mm-30) outliers start: 26 outliers final: 14 residues processed: 91 average time/residue: 0.9395 time to fit residues: 90.0035 Evaluate side-chains 87 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 400 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 15 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4955 Z= 0.157 Angle : 0.496 5.779 6729 Z= 0.261 Chirality : 0.045 0.167 753 Planarity : 0.003 0.040 862 Dihedral : 7.313 53.195 854 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.39 % Favored : 95.45 % Rotamer: Outliers : 3.97 % Allowed : 26.65 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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 (0.35), residues: 615 helix: -1.94 (1.37), residues: 12 sheet: -0.15 (0.33), residues: 234 loop : -0.28 (0.35), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 115 HIS 0.002 0.001 HIS A 336 PHE 0.019 0.002 PHE H 78 TYR 0.011 0.001 TYR A 121 ARG 0.003 0.000 ARG H 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 100 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8159 (mtm180) REVERT: A 128 LYS cc_start: 0.8150 (ptpp) cc_final: 0.7856 (ptpp) REVERT: A 162 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7768 (mm-30) outliers start: 21 outliers final: 13 residues processed: 89 average time/residue: 0.9291 time to fit residues: 87.0897 Evaluate side-chains 87 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 400 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 chunk 14 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4955 Z= 0.214 Angle : 0.514 9.037 6729 Z= 0.266 Chirality : 0.046 0.174 753 Planarity : 0.003 0.037 862 Dihedral : 7.082 54.277 854 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.23 % Favored : 95.61 % Rotamer: Outliers : 4.54 % Allowed : 27.03 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.53 (0.35), residues: 615 helix: -0.16 (2.37), residues: 6 sheet: -0.19 (0.32), residues: 239 loop : -0.39 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 34 HIS 0.002 0.001 HIS A 336 PHE 0.017 0.002 PHE H 78 TYR 0.012 0.001 TYR A 121 ARG 0.002 0.000 ARG H 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 100 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8143 (mtm180) outliers start: 24 outliers final: 16 residues processed: 91 average time/residue: 0.8519 time to fit residues: 81.8471 Evaluate side-chains 89 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.3980 chunk 58 optimal weight: 0.0570 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4955 Z= 0.194 Angle : 0.511 8.957 6729 Z= 0.265 Chirality : 0.045 0.172 753 Planarity : 0.003 0.036 862 Dihedral : 6.793 54.038 854 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.88 % Favored : 94.96 % Rotamer: Outliers : 5.29 % Allowed : 26.84 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.50 (0.34), residues: 615 helix: -0.10 (2.37), residues: 6 sheet: -0.16 (0.32), residues: 239 loop : -0.39 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 34 HIS 0.002 0.001 HIS A 336 PHE 0.017 0.002 PHE H 78 TYR 0.011 0.001 TYR A 121 ARG 0.004 0.000 ARG H 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 76 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 100 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8079 (mtm180) REVERT: A 302 ILE cc_start: 0.8751 (mp) cc_final: 0.8533 (mp) outliers start: 28 outliers final: 17 residues processed: 92 average time/residue: 0.8983 time to fit residues: 87.4145 Evaluate side-chains 91 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.0870 chunk 39 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN H 105 GLN L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4955 Z= 0.175 Angle : 0.514 9.130 6729 Z= 0.267 Chirality : 0.045 0.165 753 Planarity : 0.003 0.035 862 Dihedral : 6.584 53.782 854 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.04 % Favored : 94.80 % Rotamer: Outliers : 4.35 % Allowed : 28.17 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.45 (0.35), residues: 615 helix: -0.02 (2.35), residues: 6 sheet: -0.10 (0.33), residues: 234 loop : -0.37 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 34 HIS 0.002 0.001 HIS A 336 PHE 0.017 0.002 PHE H 78 TYR 0.011 0.001 TYR A 121 ARG 0.003 0.000 ARG H 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 78 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 100 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8147 (mtm180) REVERT: A 128 LYS cc_start: 0.7958 (ptpp) cc_final: 0.7349 (ptmt) REVERT: A 162 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7538 (mm-30) REVERT: A 302 ILE cc_start: 0.8784 (mp) cc_final: 0.8580 (mp) outliers start: 23 outliers final: 14 residues processed: 95 average time/residue: 0.8786 time to fit residues: 88.1959 Evaluate side-chains 90 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN H 105 GLN L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4955 Z= 0.262 Angle : 0.546 9.559 6729 Z= 0.284 Chirality : 0.046 0.174 753 Planarity : 0.003 0.033 862 Dihedral : 6.729 55.089 854 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.07 % Favored : 95.77 % Rotamer: Outliers : 4.35 % Allowed : 28.36 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.52 (0.34), residues: 615 helix: -0.34 (2.33), residues: 6 sheet: -0.19 (0.32), residues: 239 loop : -0.37 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS A 336 PHE 0.016 0.002 PHE H 78 TYR 0.013 0.001 TYR L 36 ARG 0.003 0.000 ARG H 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 100 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8091 (mtm180) REVERT: A 140 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8718 (tt) outliers start: 23 outliers final: 17 residues processed: 92 average time/residue: 0.9426 time to fit residues: 91.2815 Evaluate side-chains 93 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN H 105 GLN L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4955 Z= 0.282 Angle : 0.555 7.199 6729 Z= 0.290 Chirality : 0.046 0.174 753 Planarity : 0.003 0.033 862 Dihedral : 6.816 55.025 854 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.39 % Favored : 95.45 % Rotamer: Outliers : 4.54 % Allowed : 28.17 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.57 (0.34), residues: 615 helix: -0.45 (2.32), residues: 6 sheet: -0.25 (0.32), residues: 241 loop : -0.39 (0.35), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.002 0.001 HIS A 184 PHE 0.016 0.002 PHE H 78 TYR 0.013 0.001 TYR A 121 ARG 0.003 0.000 ARG H 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 73 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 100 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8091 (mtm180) REVERT: A 128 LYS cc_start: 0.7854 (ptpp) cc_final: 0.7508 (ptmt) REVERT: A 140 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8729 (tt) outliers start: 24 outliers final: 21 residues processed: 91 average time/residue: 0.9568 time to fit residues: 91.6564 Evaluate side-chains 96 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 73 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN H 105 GLN L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4955 Z= 0.191 Angle : 0.527 9.870 6729 Z= 0.273 Chirality : 0.045 0.161 753 Planarity : 0.003 0.034 862 Dihedral : 6.534 53.674 854 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.39 % Favored : 95.45 % Rotamer: Outliers : 4.73 % Allowed : 27.79 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.48 (0.35), residues: 615 helix: -0.29 (2.33), residues: 6 sheet: -0.15 (0.32), residues: 239 loop : -0.36 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS A 336 PHE 0.017 0.002 PHE H 78 TYR 0.012 0.001 TYR A 121 ARG 0.004 0.000 ARG H 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 74 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 100 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8087 (mtm180) REVERT: A 128 LYS cc_start: 0.7750 (ptpp) cc_final: 0.7397 (ptmt) REVERT: A 140 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8725 (tt) outliers start: 25 outliers final: 20 residues processed: 91 average time/residue: 0.9066 time to fit residues: 87.4441 Evaluate side-chains 93 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 71 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 0.0470 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 ASN H 105 GLN L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.115856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.093624 restraints weight = 6329.984| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.05 r_work: 0.3149 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4955 Z= 0.188 Angle : 0.513 6.689 6729 Z= 0.268 Chirality : 0.045 0.155 753 Planarity : 0.003 0.034 862 Dihedral : 6.371 53.862 854 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.07 % Favored : 95.77 % Rotamer: Outliers : 5.10 % Allowed : 27.60 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.46 (0.35), residues: 615 helix: -0.14 (2.35), residues: 6 sheet: -0.15 (0.32), residues: 239 loop : -0.34 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 34 HIS 0.002 0.001 HIS A 336 PHE 0.017 0.002 PHE H 78 TYR 0.011 0.001 TYR A 121 ARG 0.006 0.000 ARG H 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2498.05 seconds wall clock time: 44 minutes 51.86 seconds (2691.86 seconds total)