Starting phenix.real_space_refine on Sun Mar 10 20:36:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez3_28728/03_2024/8ez3_28728.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez3_28728/03_2024/8ez3_28728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez3_28728/03_2024/8ez3_28728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez3_28728/03_2024/8ez3_28728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez3_28728/03_2024/8ez3_28728.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ez3_28728/03_2024/8ez3_28728.pdb" } resolution = 2.5 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 ------------------------------------------------------------------------------- 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= 0.123 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 26 5.16 5 C 3039 2.51 5 N 839 2.21 5 O 990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ASP 31": "OD1" <-> "OD2" Residue "H TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 4894 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 969 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "L" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 815 Classifications: {'peptide': 111} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 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: 3.38, per 1000 atoms: 0.69 Number of scatterers: 4894 At special positions: 0 Unit cell: (96.46, 80.56, 93.28, 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 26 16.00 O 990 8.00 N 839 7.00 C 3039 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=2.03 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=2.03 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 329 " " NAG A 504 " - " ASN A 234 " " NAG B 1 " - " ASN A 200 " Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 779.3 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1122 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 13 sheets defined 3.5% alpha, 43.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'L' and resid 27B through 30 Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.651A pdb=" N ASN A 146 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.642A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.054A pdb=" N HIS H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.396A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AA7, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.511A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.820A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLN A 173 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.167A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.858A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.624A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.249A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 311 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.514A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER A 372 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP A 399 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LYS A 378 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) 171 hydrogen bonds defined for protein. 441 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: 1.41 Time building geometry restraints manager: 1.91 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: 1596 1.35 - 1.48: 1352 1.48 - 1.60: 2030 1.60 - 1.73: 0 1.73 - 1.85: 30 Bond restraints: 5008 Sorted by residual: bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.418 1.449 -0.031 2.00e-02 2.50e+03 2.47e+00 bond pdb=" C2 BMA B 3 " pdb=" C3 BMA B 3 " ideal model delta sigma weight residual 1.544 1.513 0.031 2.00e-02 2.50e+03 2.41e+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 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.413 1.441 -0.028 2.00e-02 2.50e+03 2.01e+00 ... (remaining 5003 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.67: 141 106.67 - 113.50: 2793 113.50 - 120.34: 1637 120.34 - 127.17: 2163 127.17 - 134.00: 76 Bond angle restraints: 6810 Sorted by residual: angle pdb=" CA CYS A 417 " pdb=" CB CYS A 417 " pdb=" SG CYS A 417 " ideal model delta sigma weight residual 114.40 127.26 -12.86 2.30e+00 1.89e-01 3.13e+01 angle pdb=" C GLY L 50 " pdb=" N ASN L 51 " pdb=" CA ASN L 51 " ideal model delta sigma weight residual 121.54 128.05 -6.51 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C HIS A 336 " pdb=" N CYS A 337 " pdb=" CA CYS A 337 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.77e+00 angle pdb=" C CYS A 417 " pdb=" CA CYS A 417 " pdb=" CB CYS A 417 " ideal model delta sigma weight residual 109.68 115.29 -5.61 1.98e+00 2.55e-01 8.04e+00 angle pdb=" C ARG A 430 " pdb=" N LYS A 431 " pdb=" CA LYS A 431 " ideal model delta sigma weight residual 121.70 126.41 -4.71 1.80e+00 3.09e-01 6.86e+00 ... (remaining 6805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.03: 2777 23.03 - 46.05: 228 46.05 - 69.08: 49 69.08 - 92.11: 14 92.11 - 115.13: 7 Dihedral angle restraints: 3075 sinusoidal: 1309 harmonic: 1766 Sorted by residual: dihedral pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual 93.00 135.77 -42.77 1 1.00e+01 1.00e-02 2.55e+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 50.93 42.07 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CA ASN L 51 " pdb=" C ASN L 51 " pdb=" N SER L 52 " pdb=" CA SER L 52 " ideal model delta harmonic sigma weight residual 180.00 158.50 21.50 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 3072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 604 0.052 - 0.105: 135 0.105 - 0.157: 27 0.157 - 0.210: 0 0.210 - 0.262: 1 Chirality restraints: 767 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 1.72e+00 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 2.66 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA VAL L 39 " pdb=" N VAL L 39 " pdb=" C VAL L 39 " pdb=" CB VAL L 39 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 764 not shown) Planarity restraints: 874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " 0.001 2.00e-02 2.50e+03 1.61e-02 3.23e+00 pdb=" CG ASN A 329 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " -0.016 2.00e-02 2.50e+03 pdb=" C1 NAG A 503 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 125 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 126 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " 0.005 2.00e-02 2.50e+03 9.49e-03 9.00e-01 pdb=" CG ASN A 329 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " 0.006 2.00e-02 2.50e+03 ... (remaining 871 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 107 2.64 - 3.21: 4308 3.21 - 3.77: 8010 3.77 - 4.34: 11814 4.34 - 4.90: 19472 Nonbonded interactions: 43711 Sorted by model distance: nonbonded pdb=" NE ARG A 403 " pdb=" OE1 GLN A 432 " model vdw 2.080 2.520 nonbonded pdb=" OG SER A 331 " pdb=" O7 NAG A 503 " model vdw 2.147 2.440 nonbonded pdb=" OG SER A 219 " pdb=" OD2 ASP A 251 " model vdw 2.220 2.440 nonbonded pdb=" ND2 ASN H 56 " pdb=" O TYR A 284 " model vdw 2.252 2.520 nonbonded pdb=" O SER H 82B" pdb=" OG SER H 82B" model vdw 2.256 2.440 ... (remaining 43706 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=0.39 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 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: 9.810 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.420 Find NCS groups from input model: 0.270 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:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 0.076 5008 Z= 0.283 Angle : 0.639 12.864 6810 Z= 0.318 Chirality : 0.046 0.262 767 Planarity : 0.003 0.040 870 Dihedral : 18.429 115.131 1920 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.85 % Allowed : 22.01 % Favored : 73.13 % 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: -0.81 (0.34), residues: 616 helix: -0.15 (2.39), residues: 6 sheet: -0.23 (0.34), residues: 223 loop : -0.71 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.011 0.002 PHE A 354 TYR 0.013 0.001 TYR A 121 ARG 0.004 0.000 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 62 time to evaluate : 0.550 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 26 residues processed: 86 average time/residue: 0.7792 time to fit residues: 71.3365 Evaluate side-chains 87 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 61 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 431 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 0.0470 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5008 Z= 0.204 Angle : 0.562 8.222 6810 Z= 0.295 Chirality : 0.046 0.200 767 Planarity : 0.004 0.041 870 Dihedral : 12.215 100.336 894 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.66 % Allowed : 21.83 % Favored : 73.51 % 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: -0.70 (0.33), residues: 616 helix: -1.35 (1.85), residues: 7 sheet: -0.04 (0.34), residues: 223 loop : -0.69 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.016 0.002 PHE A 132 TYR 0.017 0.001 TYR A 121 ARG 0.002 0.000 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 69 time to evaluate : 0.586 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 17 residues processed: 88 average time/residue: 0.7810 time to fit residues: 73.2247 Evaluate side-chains 84 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 141 ASN A 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 5008 Z= 0.373 Angle : 0.621 9.361 6810 Z= 0.323 Chirality : 0.048 0.187 767 Planarity : 0.004 0.044 870 Dihedral : 11.162 91.667 872 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.41 % Allowed : 22.57 % Favored : 72.01 % 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: -0.81 (0.33), residues: 616 helix: -1.28 (1.81), residues: 7 sheet: -0.12 (0.34), residues: 221 loop : -0.75 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.018 0.002 TYR A 121 ARG 0.002 0.000 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 61 time to evaluate : 0.584 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 24 residues processed: 81 average time/residue: 0.8457 time to fit residues: 72.7549 Evaluate side-chains 85 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 61 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5008 Z= 0.215 Angle : 0.572 10.045 6810 Z= 0.295 Chirality : 0.046 0.170 767 Planarity : 0.003 0.041 870 Dihedral : 9.909 84.209 870 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.41 % Allowed : 22.20 % Favored : 72.39 % 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: -0.74 (0.33), residues: 616 helix: -1.20 (1.84), residues: 7 sheet: -0.15 (0.33), residues: 228 loop : -0.65 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.015 0.001 TYR A 121 ARG 0.002 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 65 time to evaluate : 0.510 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 23 residues processed: 85 average time/residue: 0.7913 time to fit residues: 71.6114 Evaluate side-chains 86 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 63 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 91 GLN A 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5008 Z= 0.263 Angle : 0.585 10.516 6810 Z= 0.299 Chirality : 0.046 0.185 767 Planarity : 0.004 0.046 870 Dihedral : 9.291 71.852 869 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 6.16 % Allowed : 21.46 % Favored : 72.39 % 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: -0.76 (0.33), residues: 616 helix: -1.23 (1.80), residues: 7 sheet: -0.18 (0.33), residues: 228 loop : -0.66 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.016 0.002 TYR A 121 ARG 0.008 0.000 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 63 time to evaluate : 0.599 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 27 residues processed: 86 average time/residue: 0.8194 time to fit residues: 74.9234 Evaluate side-chains 88 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 61 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 91 GLN A 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5008 Z= 0.282 Angle : 0.586 9.402 6810 Z= 0.300 Chirality : 0.046 0.190 767 Planarity : 0.004 0.043 870 Dihedral : 8.710 58.851 869 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 6.16 % Allowed : 22.01 % Favored : 71.83 % 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: -0.78 (0.33), residues: 616 helix: -1.16 (1.78), residues: 7 sheet: -0.20 (0.33), residues: 228 loop : -0.67 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.016 0.002 TYR A 121 ARG 0.003 0.000 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 62 time to evaluate : 0.513 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 24 residues processed: 87 average time/residue: 0.8239 time to fit residues: 76.1575 Evaluate side-chains 85 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 61 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 91 GLN A 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5008 Z= 0.224 Angle : 0.554 6.559 6810 Z= 0.287 Chirality : 0.046 0.161 767 Planarity : 0.003 0.041 870 Dihedral : 8.215 57.991 864 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.41 % Allowed : 22.20 % Favored : 72.39 % 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: -0.76 (0.33), residues: 616 helix: -1.11 (1.82), residues: 7 sheet: -0.15 (0.33), residues: 229 loop : -0.69 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.015 0.001 TYR A 121 ARG 0.003 0.000 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 64 time to evaluate : 0.563 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 23 residues processed: 85 average time/residue: 0.8352 time to fit residues: 75.2759 Evaluate side-chains 85 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 62 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 0.0010 chunk 46 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5008 Z= 0.185 Angle : 0.538 6.533 6810 Z= 0.280 Chirality : 0.045 0.146 767 Planarity : 0.003 0.041 870 Dihedral : 7.893 58.429 863 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.85 % Allowed : 23.13 % Favored : 72.01 % 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: -0.71 (0.33), residues: 616 helix: -1.10 (1.83), residues: 7 sheet: -0.10 (0.33), residues: 229 loop : -0.67 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.012 0.002 PHE A 354 TYR 0.014 0.001 TYR A 121 ARG 0.002 0.000 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 64 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: L 72 SER cc_start: 0.8527 (OUTLIER) cc_final: 0.8297 (t) outliers start: 26 outliers final: 21 residues processed: 81 average time/residue: 0.8375 time to fit residues: 72.0391 Evaluate side-chains 84 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 91 GLN A 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5008 Z= 0.296 Angle : 0.569 6.580 6810 Z= 0.297 Chirality : 0.046 0.150 767 Planarity : 0.004 0.043 870 Dihedral : 7.704 58.070 862 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.85 % Allowed : 23.69 % 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: -0.72 (0.33), residues: 616 helix: -1.20 (1.75), residues: 7 sheet: -0.16 (0.33), residues: 228 loop : -0.63 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 178 HIS 0.002 0.001 HIS L 34 PHE 0.014 0.002 PHE A 354 TYR 0.016 0.002 TYR A 121 ARG 0.004 0.000 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 60 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: L 72 SER cc_start: 0.8566 (OUTLIER) cc_final: 0.8333 (t) REVERT: A 140 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8851 (tp) outliers start: 26 outliers final: 21 residues processed: 79 average time/residue: 0.8027 time to fit residues: 67.5009 Evaluate side-chains 81 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 58 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 91 GLN A 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5008 Z= 0.260 Angle : 0.559 6.566 6810 Z= 0.292 Chirality : 0.046 0.162 767 Planarity : 0.003 0.042 870 Dihedral : 7.400 57.693 862 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.48 % Allowed : 24.07 % 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: -0.71 (0.33), residues: 616 helix: -1.09 (1.83), residues: 7 sheet: -0.15 (0.33), residues: 228 loop : -0.62 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.014 0.002 PHE A 354 TYR 0.016 0.001 TYR A 121 ARG 0.003 0.000 ARG H 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 59 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: L 72 SER cc_start: 0.8558 (OUTLIER) cc_final: 0.8331 (t) REVERT: A 140 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8981 (tp) outliers start: 24 outliers final: 20 residues processed: 77 average time/residue: 0.8211 time to fit residues: 67.2287 Evaluate side-chains 81 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 59 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 91 GLN A 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.118030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.088321 restraints weight = 5732.323| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.17 r_work: 0.2917 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5008 Z= 0.269 Angle : 0.561 6.562 6810 Z= 0.293 Chirality : 0.046 0.148 767 Planarity : 0.004 0.042 870 Dihedral : 7.235 57.463 862 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.66 % Allowed : 23.88 % 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: -0.72 (0.33), residues: 616 helix: -1.08 (1.83), residues: 7 sheet: -0.16 (0.33), residues: 228 loop : -0.63 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.014 0.002 PHE A 354 TYR 0.016 0.001 TYR A 121 ARG 0.004 0.000 ARG H 81 =============================================================================== Job complete usr+sys time: 2173.83 seconds wall clock time: 39 minutes 23.90 seconds (2363.90 seconds total)