Starting phenix.real_space_refine on Tue Jun 10 03:21:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qpc_14117/06_2025/7qpc_14117_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qpc_14117/06_2025/7qpc_14117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qpc_14117/06_2025/7qpc_14117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qpc_14117/06_2025/7qpc_14117.map" model { file = "/net/cci-nas-00/data/ceres_data/7qpc_14117/06_2025/7qpc_14117_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qpc_14117/06_2025/7qpc_14117_trim.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.040 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 34 5.16 5 C 3524 2.51 5 N 804 2.21 5 O 926 1.98 5 H 5540 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10830 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5246 Classifications: {'peptide': 327} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "B" Number of atoms: 5246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5246 Classifications: {'peptide': 327} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'DLP': 1, 'E7O': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'DLP': 1, 'E7O': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 96 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 90 Classifications: {'water': 30} Link IDs: {None: 29} Time building chain proxies: 5.39, per 1000 atoms: 0.50 Number of scatterers: 10830 At special positions: 0 Unit cell: (91.874, 90.58, 68.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 2 15.00 O 926 8.00 N 804 7.00 C 3524 6.00 H 5540 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 822.5 milliseconds 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1216 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 85.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 3 through 29 Proline residue: A 16 - end of helix removed outlier: 3.924A pdb=" N MET A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY A 24 " --> pdb=" O SER A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 60 removed outlier: 4.693A pdb=" N ILE A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 63 through 67 Processing helix chain 'A' and resid 68 through 93 removed outlier: 3.592A pdb=" N ILE A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 122 through 148 removed outlier: 6.931A pdb=" N ASP A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N GLU A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLN A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 removed outlier: 3.544A pdb=" N LEU A 154 " --> pdb=" O TYR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 220 removed outlier: 3.677A pdb=" N ILE A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 240 removed outlier: 3.738A pdb=" N TYR A 225 " --> pdb=" O ASN A 221 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.844A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 274 removed outlier: 3.595A pdb=" N GLN A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 294 through 308 Processing helix chain 'A' and resid 313 through 322 Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.502A pdb=" N ILE A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 366 removed outlier: 3.593A pdb=" N THR A 357 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 30 Proline residue: B 16 - end of helix removed outlier: 3.934A pdb=" N MET B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 60 removed outlier: 4.956A pdb=" N ILE B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Proline residue: B 52 - end of helix Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 68 through 91 removed outlier: 3.879A pdb=" N VAL B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 Processing helix chain 'B' and resid 122 through 164 removed outlier: 6.877A pdb=" N ASP B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N GLU B 133 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA B 135 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN B 140 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TRP B 149 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TYR B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 152 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 220 removed outlier: 3.709A pdb=" N ILE B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 240 removed outlier: 3.579A pdb=" N TYR B 225 " --> pdb=" O ASN B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 257 removed outlier: 3.869A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 274 removed outlier: 3.505A pdb=" N GLN B 274 " --> pdb=" O PHE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.602A pdb=" N ILE B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 288 " --> pdb=" O MET B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 308 Processing helix chain 'B' and resid 313 through 322 Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 339 through 353 Processing helix chain 'B' and resid 353 through 366 removed outlier: 3.600A pdb=" N ASP B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.82 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5534 1.03 - 1.23: 12 1.23 - 1.42: 2108 1.42 - 1.62: 3176 1.62 - 1.81: 62 Bond restraints: 10892 Sorted by residual: bond pdb=" C12 E7O A 401 " pdb=" N11 E7O A 401 " ideal model delta sigma weight residual 1.347 1.459 -0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C12 E7O B 401 " pdb=" N11 E7O B 401 " ideal model delta sigma weight residual 1.347 1.458 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C10 E7O B 401 " pdb=" N11 E7O B 401 " ideal model delta sigma weight residual 1.399 1.461 -0.062 2.00e-02 2.50e+03 9.58e+00 bond pdb=" C10 E7O A 401 " pdb=" N11 E7O A 401 " ideal model delta sigma weight residual 1.399 1.459 -0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" O4P DLP A 402 " pdb=" P DLP A 402 " ideal model delta sigma weight residual 1.649 1.596 0.053 2.00e-02 2.50e+03 7.13e+00 ... (remaining 10887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 19399 2.13 - 4.27: 190 4.27 - 6.40: 18 6.40 - 8.53: 1 8.53 - 10.66: 2 Bond angle restraints: 19610 Sorted by residual: angle pdb=" N LEU A 313 " pdb=" CA LEU A 313 " pdb=" C LEU A 313 " ideal model delta sigma weight residual 114.04 109.16 4.88 1.24e+00 6.50e-01 1.55e+01 angle pdb=" N ILE A 137 " pdb=" CA ILE A 137 " pdb=" C ILE A 137 " ideal model delta sigma weight residual 111.81 108.61 3.20 8.60e-01 1.35e+00 1.39e+01 angle pdb=" O3P DLP A 402 " pdb=" P DLP A 402 " pdb=" O4P DLP A 402 " ideal model delta sigma weight residual 93.58 104.24 -10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" O3P DLP B 402 " pdb=" P DLP B 402 " pdb=" O4P DLP B 402 " ideal model delta sigma weight residual 93.58 104.24 -10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" C VAL B 328 " pdb=" CA VAL B 328 " pdb=" CB VAL B 328 " ideal model delta sigma weight residual 114.35 111.05 3.30 1.06e+00 8.90e-01 9.72e+00 ... (remaining 19605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.78: 4619 20.78 - 41.56: 315 41.56 - 62.35: 104 62.35 - 83.13: 4 83.13 - 103.91: 2 Dihedral angle restraints: 5044 sinusoidal: 2776 harmonic: 2268 Sorted by residual: dihedral pdb=" CA THR B 108 " pdb=" C THR B 108 " pdb=" N GLY B 109 " pdb=" CA GLY B 109 " ideal model delta harmonic sigma weight residual 180.00 157.52 22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" N DLP B 402 " pdb=" C4 DLP B 402 " pdb=" C5 DLP B 402 " pdb=" O4P DLP B 402 " ideal model delta sinusoidal sigma weight residual -71.05 -174.96 103.91 1 3.00e+01 1.11e-03 1.32e+01 dihedral pdb=" N DLP A 402 " pdb=" C4 DLP A 402 " pdb=" C5 DLP A 402 " pdb=" O4P DLP A 402 " ideal model delta sinusoidal sigma weight residual -71.05 -174.81 103.76 1 3.00e+01 1.11e-03 1.32e+01 ... (remaining 5041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 690 0.041 - 0.083: 141 0.083 - 0.124: 29 0.124 - 0.165: 0 0.165 - 0.207: 2 Chirality restraints: 862 Sorted by residual: chirality pdb=" C2 DLP A 402 " pdb=" C1 DLP A 402 " pdb=" C3 DLP A 402 " pdb=" O2 DLP A 402 " both_signs ideal model delta sigma weight residual False -2.35 -2.56 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C2 DLP B 402 " pdb=" C1 DLP B 402 " pdb=" C3 DLP B 402 " pdb=" O2 DLP B 402 " both_signs ideal model delta sigma weight residual False -2.35 -2.56 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE A 2 " pdb=" N ILE A 2 " pdb=" C ILE A 2 " pdb=" CB ILE A 2 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.16e-01 ... (remaining 859 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 355 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO B 356 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 356 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 356 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 46 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C VAL A 46 " 0.023 2.00e-02 2.50e+03 pdb=" O VAL A 46 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA A 47 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 291 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C LEU B 291 " 0.023 2.00e-02 2.50e+03 pdb=" O LEU B 291 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS B 292 " -0.008 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 1390 2.26 - 2.84: 24759 2.84 - 3.43: 28901 3.43 - 4.01: 39628 4.01 - 4.60: 61268 Nonbonded interactions: 155946 Sorted by model distance: nonbonded pdb=" OE2 GLU B 158 " pdb=" HH TYR B 336 " model vdw 1.671 2.450 nonbonded pdb=" H SER A 35 " pdb=" OE1 GLN A 38 " model vdw 1.695 2.450 nonbonded pdb="HD22 ASN B 62 " pdb=" OE1 GLU B 139 " model vdw 1.713 2.450 nonbonded pdb=" O SER A 50 " pdb=" H LEU A 54 " model vdw 1.728 2.450 nonbonded pdb=" H ASN B 117 " pdb=" O PRO B 324 " model vdw 1.729 2.450 ... (remaining 155941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 0.210 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.230 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 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 0.112 5352 Z= 0.206 Angle : 0.624 10.663 7252 Z= 0.303 Chirality : 0.036 0.207 862 Planarity : 0.003 0.035 858 Dihedral : 15.004 103.909 1948 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.35), residues: 646 helix: 1.58 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -1.06 (0.54), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 233 HIS 0.001 0.000 HIS A 94 PHE 0.007 0.001 PHE B 330 TYR 0.005 0.001 TYR B 305 ARG 0.007 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.13489 ( 366) hydrogen bonds : angle 5.36417 ( 1086) covalent geometry : bond 0.00418 ( 5352) covalent geometry : angle 0.62406 ( 7252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.4031 time to fit residues: 56.7264 Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.124132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.106365 restraints weight = 18844.896| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.63 r_work: 0.3003 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5352 Z= 0.153 Angle : 0.547 4.795 7252 Z= 0.285 Chirality : 0.036 0.125 862 Planarity : 0.004 0.039 858 Dihedral : 10.781 107.829 784 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.36 % Allowed : 5.78 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.34), residues: 646 helix: 1.55 (0.24), residues: 520 sheet: None (None), residues: 0 loop : -1.42 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 93 HIS 0.006 0.001 HIS B 339 PHE 0.010 0.001 PHE A 314 TYR 0.009 0.001 TYR A 362 ARG 0.001 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 366) hydrogen bonds : angle 4.61939 ( 1086) covalent geometry : bond 0.00349 ( 5352) covalent geometry : angle 0.54700 ( 7252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8243 (mt-10) outliers start: 2 outliers final: 2 residues processed: 104 average time/residue: 0.3551 time to fit residues: 48.5152 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.0970 chunk 10 optimal weight: 0.0980 chunk 23 optimal weight: 0.2980 chunk 61 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.107124 restraints weight = 18955.072| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.63 r_work: 0.3016 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5352 Z= 0.110 Angle : 0.509 4.638 7252 Z= 0.262 Chirality : 0.035 0.126 862 Planarity : 0.004 0.038 858 Dihedral : 10.511 102.094 784 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.54 % Allowed : 6.68 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.34), residues: 646 helix: 1.63 (0.24), residues: 522 sheet: None (None), residues: 0 loop : -1.54 (0.54), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.003 0.001 HIS B 339 PHE 0.009 0.001 PHE A 314 TYR 0.008 0.001 TYR A 362 ARG 0.002 0.000 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 366) hydrogen bonds : angle 4.42793 ( 1086) covalent geometry : bond 0.00245 ( 5352) covalent geometry : angle 0.50928 ( 7252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8285 (mt-10) REVERT: B 62 ASN cc_start: 0.6864 (m110) cc_final: 0.6239 (m110) outliers start: 3 outliers final: 2 residues processed: 103 average time/residue: 0.4034 time to fit residues: 55.1050 Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.122556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.105056 restraints weight = 18943.289| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.59 r_work: 0.2984 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5352 Z= 0.147 Angle : 0.535 4.736 7252 Z= 0.276 Chirality : 0.036 0.132 862 Planarity : 0.004 0.043 858 Dihedral : 10.496 94.576 784 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.36 % Allowed : 8.84 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.34), residues: 646 helix: 1.53 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.58 (0.53), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 233 HIS 0.003 0.001 HIS B 339 PHE 0.009 0.001 PHE A 330 TYR 0.007 0.001 TYR A 362 ARG 0.003 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 366) hydrogen bonds : angle 4.37175 ( 1086) covalent geometry : bond 0.00344 ( 5352) covalent geometry : angle 0.53477 ( 7252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8233 (mt-10) outliers start: 2 outliers final: 1 residues processed: 105 average time/residue: 0.3663 time to fit residues: 50.5384 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 37 optimal weight: 0.0870 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.123063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.105200 restraints weight = 18933.446| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.63 r_work: 0.2986 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5352 Z= 0.121 Angle : 0.518 4.580 7252 Z= 0.266 Chirality : 0.035 0.140 862 Planarity : 0.004 0.042 858 Dihedral : 10.171 89.600 784 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.36 % Allowed : 11.01 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.34), residues: 646 helix: 1.60 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.66 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.002 0.001 HIS B 339 PHE 0.010 0.001 PHE A 314 TYR 0.006 0.001 TYR A 362 ARG 0.004 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 366) hydrogen bonds : angle 4.26788 ( 1086) covalent geometry : bond 0.00274 ( 5352) covalent geometry : angle 0.51826 ( 7252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7398 (tt0) outliers start: 2 outliers final: 1 residues processed: 105 average time/residue: 0.3644 time to fit residues: 50.0664 Evaluate side-chains 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 139 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.103646 restraints weight = 19269.213| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.64 r_work: 0.2962 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5352 Z= 0.157 Angle : 0.535 4.447 7252 Z= 0.277 Chirality : 0.036 0.166 862 Planarity : 0.004 0.043 858 Dihedral : 10.245 88.636 784 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.36 % Allowed : 12.27 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.34), residues: 646 helix: 1.53 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.76 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.003 0.001 HIS B 237 PHE 0.010 0.001 PHE B 330 TYR 0.007 0.001 TYR A 362 ARG 0.004 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 366) hydrogen bonds : angle 4.28173 ( 1086) covalent geometry : bond 0.00368 ( 5352) covalent geometry : angle 0.53496 ( 7252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8658 (mm) cc_final: 0.8257 (mm) REVERT: B 284 MET cc_start: 0.7955 (mmm) cc_final: 0.7742 (mmm) outliers start: 2 outliers final: 1 residues processed: 102 average time/residue: 0.3398 time to fit residues: 46.4469 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 3 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.122196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.104279 restraints weight = 19378.325| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.65 r_work: 0.2973 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5352 Z= 0.123 Angle : 0.519 4.396 7252 Z= 0.267 Chirality : 0.035 0.147 862 Planarity : 0.004 0.042 858 Dihedral : 10.030 87.055 784 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.18 % Allowed : 12.27 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.34), residues: 646 helix: 1.59 (0.24), residues: 518 sheet: None (None), residues: 0 loop : -1.73 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 233 HIS 0.002 0.001 HIS B 339 PHE 0.010 0.001 PHE A 314 TYR 0.005 0.001 TYR A 361 ARG 0.005 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03419 ( 366) hydrogen bonds : angle 4.21710 ( 1086) covalent geometry : bond 0.00284 ( 5352) covalent geometry : angle 0.51890 ( 7252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8645 (mm) cc_final: 0.8245 (mm) REVERT: B 284 MET cc_start: 0.7980 (mmm) cc_final: 0.7778 (mmm) outliers start: 1 outliers final: 1 residues processed: 103 average time/residue: 0.3526 time to fit residues: 47.8819 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.121361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.103380 restraints weight = 18986.174| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.64 r_work: 0.2958 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5352 Z= 0.147 Angle : 0.533 4.531 7252 Z= 0.275 Chirality : 0.036 0.131 862 Planarity : 0.004 0.042 858 Dihedral : 10.045 85.759 784 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.36 % Allowed : 12.45 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.34), residues: 646 helix: 1.53 (0.24), residues: 518 sheet: None (None), residues: 0 loop : -1.78 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 93 HIS 0.002 0.001 HIS B 237 PHE 0.010 0.001 PHE B 330 TYR 0.006 0.001 TYR A 361 ARG 0.006 0.001 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 366) hydrogen bonds : angle 4.22587 ( 1086) covalent geometry : bond 0.00347 ( 5352) covalent geometry : angle 0.53305 ( 7252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8685 (mm) cc_final: 0.8293 (mm) REVERT: B 262 MET cc_start: 0.7981 (ttt) cc_final: 0.7737 (ttm) REVERT: B 284 MET cc_start: 0.7990 (mmm) cc_final: 0.7790 (mmm) outliers start: 2 outliers final: 2 residues processed: 101 average time/residue: 0.3433 time to fit residues: 46.2153 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 139 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.121469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.103550 restraints weight = 19262.619| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.63 r_work: 0.2963 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5352 Z= 0.130 Angle : 0.523 4.547 7252 Z= 0.269 Chirality : 0.035 0.127 862 Planarity : 0.004 0.039 858 Dihedral : 9.940 84.343 784 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.36 % Allowed : 12.82 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.34), residues: 646 helix: 1.57 (0.24), residues: 518 sheet: None (None), residues: 0 loop : -1.78 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.002 0.001 HIS B 339 PHE 0.010 0.001 PHE B 330 TYR 0.006 0.001 TYR A 361 ARG 0.006 0.001 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 366) hydrogen bonds : angle 4.18289 ( 1086) covalent geometry : bond 0.00303 ( 5352) covalent geometry : angle 0.52333 ( 7252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8686 (mm) cc_final: 0.8267 (mm) outliers start: 2 outliers final: 2 residues processed: 103 average time/residue: 0.3455 time to fit residues: 47.2896 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 139 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.120748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.102743 restraints weight = 19172.880| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.64 r_work: 0.2949 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5352 Z= 0.144 Angle : 0.537 4.955 7252 Z= 0.275 Chirality : 0.036 0.127 862 Planarity : 0.004 0.040 858 Dihedral : 9.982 83.413 784 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.36 % Allowed : 13.54 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.34), residues: 646 helix: 1.54 (0.24), residues: 518 sheet: None (None), residues: 0 loop : -1.81 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.002 0.001 HIS B 237 PHE 0.018 0.001 PHE B 92 TYR 0.006 0.001 TYR A 361 ARG 0.006 0.001 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 366) hydrogen bonds : angle 4.18743 ( 1086) covalent geometry : bond 0.00339 ( 5352) covalent geometry : angle 0.53696 ( 7252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8689 (mm) cc_final: 0.8267 (mm) outliers start: 2 outliers final: 2 residues processed: 100 average time/residue: 0.3463 time to fit residues: 46.3253 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 139 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.103654 restraints weight = 19034.506| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.63 r_work: 0.2966 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5352 Z= 0.123 Angle : 0.526 4.556 7252 Z= 0.269 Chirality : 0.035 0.126 862 Planarity : 0.004 0.039 858 Dihedral : 9.850 82.535 784 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.54 % Allowed : 13.36 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.34), residues: 646 helix: 1.59 (0.24), residues: 518 sheet: None (None), residues: 0 loop : -1.79 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.002 0.001 HIS B 339 PHE 0.010 0.001 PHE B 330 TYR 0.005 0.001 TYR A 361 ARG 0.006 0.001 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 366) hydrogen bonds : angle 4.14585 ( 1086) covalent geometry : bond 0.00287 ( 5352) covalent geometry : angle 0.52563 ( 7252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5684.92 seconds wall clock time: 98 minutes 29.47 seconds (5909.47 seconds total)