Starting phenix.real_space_refine on Wed Sep 17 20:49:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qpc_14117/09_2025/7qpc_14117_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qpc_14117/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7qpc_14117/09_2025/7qpc_14117_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qpc_14117/09_2025/7qpc_14117_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qpc_14117/09_2025/7qpc_14117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qpc_14117/09_2025/7qpc_14117.map" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.59, per 1000 atoms: 0.24 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: 1.16 Conformation dependent library (CDL) restraints added in 258.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.26 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: 2.52 Time building geometry restraints manager: 1.54 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: 0.00 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: 0.750 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: 0.070 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 12.910 Find NCS groups from input model: 0.110 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.400 ------------------------------------------------------------------------------- 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 : 5.91 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG B 216 TYR 0.005 0.001 TYR B 305 PHE 0.007 0.001 PHE B 330 TRP 0.004 0.001 TRP B 233 HIS 0.001 0.000 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 5352) covalent geometry : angle 0.62406 ( 7252) hydrogen bonds : bond 0.13489 ( 366) hydrogen bonds : angle 5.36417 ( 1086) *********************** 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 : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1978 time to fit residues: 27.7388 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 : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.124751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.107423 restraints weight = 18835.880| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.57 r_work: 0.3023 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.0811 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= 0.138 Angle : 0.541 4.847 7252 Z= 0.281 Chirality : 0.036 0.125 862 Planarity : 0.004 0.038 858 Dihedral : 10.733 108.290 784 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.36 % Allowed : 5.60 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.34), residues: 646 helix: 1.59 (0.24), residues: 520 sheet: None (None), residues: 0 loop : -1.41 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 216 TYR 0.010 0.001 TYR A 362 PHE 0.011 0.001 PHE A 314 TRP 0.007 0.001 TRP A 93 HIS 0.006 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5352) covalent geometry : angle 0.54084 ( 7252) hydrogen bonds : bond 0.04084 ( 366) hydrogen bonds : angle 4.58893 ( 1086) *********************** 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 : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8221 (mt-10) REVERT: B 337 ASN cc_start: 0.8701 (t0) cc_final: 0.8493 (t0) outliers start: 2 outliers final: 2 residues processed: 104 average time/residue: 0.1719 time to fit residues: 23.4624 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 : 0.208 ------------------------------------------------------------------------------- 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 11 optimal weight: 0.0470 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.124507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.106640 restraints weight = 19065.288| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.64 r_work: 0.3006 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5352 Z= 0.117 Angle : 0.510 4.649 7252 Z= 0.262 Chirality : 0.035 0.125 862 Planarity : 0.004 0.041 858 Dihedral : 10.511 100.159 784 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.36 % Allowed : 6.50 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.34), residues: 646 helix: 1.65 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.53 (0.54), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 216 TYR 0.008 0.001 TYR A 362 PHE 0.009 0.001 PHE A 314 TRP 0.006 0.001 TRP A 93 HIS 0.002 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 5352) covalent geometry : angle 0.51006 ( 7252) hydrogen bonds : bond 0.03751 ( 366) hydrogen bonds : angle 4.38521 ( 1086) *********************** 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 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8188 (mt-10) REVERT: B 62 ASN cc_start: 0.6851 (m110) cc_final: 0.6277 (m110) outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 0.1702 time to fit residues: 23.1185 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 : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 18 optimal weight: 0.1980 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.124556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.106684 restraints weight = 18897.966| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.64 r_work: 0.3009 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1099 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= 0.109 Angle : 0.510 4.580 7252 Z= 0.261 Chirality : 0.035 0.128 862 Planarity : 0.004 0.042 858 Dihedral : 10.351 94.617 784 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.36 % Allowed : 8.30 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.34), residues: 646 helix: 1.65 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.52 (0.54), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 216 TYR 0.006 0.001 TYR A 362 PHE 0.009 0.001 PHE B 330 TRP 0.007 0.001 TRP B 233 HIS 0.003 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 5352) covalent geometry : angle 0.50966 ( 7252) hydrogen bonds : bond 0.03451 ( 366) hydrogen bonds : angle 4.27772 ( 1086) *********************** 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 : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8181 (mt-10) REVERT: B 139 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7306 (tt0) outliers start: 2 outliers final: 1 residues processed: 105 average time/residue: 0.1797 time to fit residues: 24.8435 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 : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 139 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.123441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.105670 restraints weight = 18842.941| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.61 r_work: 0.2994 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1301 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= 0.125 Angle : 0.515 4.811 7252 Z= 0.264 Chirality : 0.036 0.149 862 Planarity : 0.004 0.044 858 Dihedral : 10.105 89.808 784 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.36 % Allowed : 9.75 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.34), residues: 646 helix: 1.66 (0.24), residues: 518 sheet: None (None), residues: 0 loop : -1.62 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 216 TYR 0.006 0.001 TYR A 362 PHE 0.009 0.001 PHE B 330 TRP 0.007 0.001 TRP A 93 HIS 0.002 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5352) covalent geometry : angle 0.51543 ( 7252) hydrogen bonds : bond 0.03402 ( 366) hydrogen bonds : angle 4.21892 ( 1086) *********************** 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 : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 105 average time/residue: 0.1718 time to fit residues: 23.7076 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 : 0.281 ------------------------------------------------------------------------------- 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 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.123526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.105763 restraints weight = 19030.499| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.62 r_work: 0.2996 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5352 Z= 0.116 Angle : 0.512 4.419 7252 Z= 0.262 Chirality : 0.035 0.150 862 Planarity : 0.004 0.043 858 Dihedral : 9.838 87.842 784 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.54 % Allowed : 11.73 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.34), residues: 646 helix: 1.72 (0.24), residues: 518 sheet: None (None), residues: 0 loop : -1.69 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 216 TYR 0.007 0.001 TYR B 361 PHE 0.009 0.001 PHE A 314 TRP 0.007 0.001 TRP A 93 HIS 0.002 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 5352) covalent geometry : angle 0.51210 ( 7252) hydrogen bonds : bond 0.03312 ( 366) hydrogen bonds : angle 4.15226 ( 1086) *********************** 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 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 284 MET cc_start: 0.7954 (mmm) cc_final: 0.7738 (mmm) outliers start: 3 outliers final: 1 residues processed: 103 average time/residue: 0.1760 time to fit residues: 23.9262 Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 45 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.122324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.104484 restraints weight = 19044.110| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.63 r_work: 0.2974 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1534 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= 0.143 Angle : 0.531 4.503 7252 Z= 0.274 Chirality : 0.036 0.144 862 Planarity : 0.004 0.043 858 Dihedral : 9.914 87.077 784 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.18 % Allowed : 12.09 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.34), residues: 646 helix: 1.63 (0.24), residues: 518 sheet: None (None), residues: 0 loop : -1.74 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 216 TYR 0.006 0.001 TYR A 362 PHE 0.009 0.001 PHE B 330 TRP 0.007 0.001 TRP B 233 HIS 0.002 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5352) covalent geometry : angle 0.53107 ( 7252) hydrogen bonds : bond 0.03370 ( 366) hydrogen bonds : angle 4.18432 ( 1086) *********************** 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 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8652 (mm) cc_final: 0.8256 (mm) REVERT: B 284 MET cc_start: 0.7953 (mmm) cc_final: 0.7746 (mmm) outliers start: 1 outliers final: 1 residues processed: 102 average time/residue: 0.1807 time to fit residues: 24.2129 Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 4 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 0.0040 chunk 43 optimal weight: 0.8980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.122724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.104839 restraints weight = 19098.686| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.63 r_work: 0.2985 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1568 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= 0.122 Angle : 0.518 4.503 7252 Z= 0.266 Chirality : 0.035 0.126 862 Planarity : 0.004 0.042 858 Dihedral : 9.738 85.577 784 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.34), residues: 646 helix: 1.68 (0.24), residues: 518 sheet: None (None), residues: 0 loop : -1.74 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 216 TYR 0.009 0.001 TYR B 361 PHE 0.010 0.001 PHE A 314 TRP 0.007 0.001 TRP A 93 HIS 0.002 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 5352) covalent geometry : angle 0.51805 ( 7252) hydrogen bonds : bond 0.03290 ( 366) hydrogen bonds : angle 4.13294 ( 1086) *********************** 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 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8627 (mm) cc_final: 0.8228 (mm) REVERT: B 262 MET cc_start: 0.7970 (ttt) cc_final: 0.7730 (ttm) REVERT: B 284 MET cc_start: 0.8026 (mmm) cc_final: 0.7809 (mmm) outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.1841 time to fit residues: 24.0513 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 : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 2 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.123808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.105983 restraints weight = 18841.285| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.62 r_work: 0.3000 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5352 Z= 0.101 Angle : 0.505 4.587 7252 Z= 0.258 Chirality : 0.035 0.127 862 Planarity : 0.004 0.039 858 Dihedral : 9.392 83.619 784 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.18 % Allowed : 12.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.35), residues: 646 helix: 1.74 (0.24), residues: 520 sheet: None (None), residues: 0 loop : -1.61 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 216 TYR 0.005 0.001 TYR A 361 PHE 0.009 0.001 PHE B 330 TRP 0.008 0.001 TRP A 93 HIS 0.002 0.000 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 5352) covalent geometry : angle 0.50493 ( 7252) hydrogen bonds : bond 0.03138 ( 366) hydrogen bonds : angle 4.03668 ( 1086) *********************** 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: 1 poor density : 103 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 TYR cc_start: 0.8292 (m-10) cc_final: 0.8068 (m-10) REVERT: B 103 LEU cc_start: 0.8698 (tt) cc_final: 0.8495 (tt) REVERT: B 120 ILE cc_start: 0.8609 (mm) cc_final: 0.8216 (mm) REVERT: B 284 MET cc_start: 0.8007 (mmm) cc_final: 0.7800 (mmm) outliers start: 1 outliers final: 1 residues processed: 104 average time/residue: 0.1726 time to fit residues: 23.5078 Evaluate side-chains 97 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 40 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.122925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.104953 restraints weight = 19076.362| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.65 r_work: 0.2984 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5352 Z= 0.124 Angle : 0.524 4.691 7252 Z= 0.268 Chirality : 0.035 0.126 862 Planarity : 0.004 0.040 858 Dihedral : 9.424 82.804 784 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.54 % Allowed : 13.54 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.34), residues: 646 helix: 1.69 (0.24), residues: 520 sheet: None (None), residues: 0 loop : -1.63 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 216 TYR 0.008 0.001 TYR B 361 PHE 0.010 0.001 PHE A 330 TRP 0.009 0.001 TRP A 93 HIS 0.002 0.000 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5352) covalent geometry : angle 0.52399 ( 7252) hydrogen bonds : bond 0.03191 ( 366) hydrogen bonds : angle 4.04833 ( 1086) ********************** 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 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 TYR cc_start: 0.8290 (m-10) cc_final: 0.8059 (m-10) REVERT: B 103 LEU cc_start: 0.8711 (tt) cc_final: 0.8511 (tt) REVERT: B 120 ILE cc_start: 0.8642 (mm) cc_final: 0.8216 (mm) REVERT: B 284 MET cc_start: 0.8026 (mmm) cc_final: 0.7818 (mmm) outliers start: 3 outliers final: 1 residues processed: 98 average time/residue: 0.1570 time to fit residues: 20.4151 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 : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 39 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.122933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.104817 restraints weight = 19169.275| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.65 r_work: 0.3009 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1723 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= 0.118 Angle : 0.517 4.612 7252 Z= 0.264 Chirality : 0.035 0.126 862 Planarity : 0.004 0.039 858 Dihedral : 9.378 82.015 784 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.18 % Allowed : 13.90 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.35), residues: 646 helix: 1.70 (0.24), residues: 520 sheet: None (None), residues: 0 loop : -1.62 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 216 TYR 0.005 0.001 TYR A 305 PHE 0.010 0.001 PHE A 330 TRP 0.008 0.001 TRP A 93 HIS 0.002 0.000 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 5352) covalent geometry : angle 0.51718 ( 7252) hydrogen bonds : bond 0.03152 ( 366) hydrogen bonds : angle 4.03554 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2883.13 seconds wall clock time: 49 minutes 35.90 seconds (2975.90 seconds total)